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AQA Hardware Manual - Conquer Scientific

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1. FINNIGAN ACA Spares 8 3 Spares Part description Part number Number or Part category amount of each part contained in the pack 3 m line extender cable C773A 1 spare insert retaining latch FM100485 1 spare adjuster thumb nut FM100487 1 spare 34 OD x 12 ID clear hose FM100595 3 meters spare 6 mm PTFE tube PDMO00129 3 meters spare 3 8 ID PVC hose PDM00130 3 meters spare 1 16 x 0 13 mm ID red PEEK tubing PDM00134 1 meter spare loop back connector TDAT106 1 spare thumb screw vacuum line clamp 9227 64 1 spare LC fitting clamp 9227 100 1 spare source block voltage contact pin 9227 113 1 spare flow disrupter pin 9227 119 1 spare M4 shakeproof washer 1150406 10 spare source voltage contact washer 1150705 10 spare M2 plain M3 x 10 countersunk st stl screw 5311017 10 spare source voltage contact screw 5312004 10 spare M2 x 4LG ch head st stl M4 x 10 cap head st stl screw 5313015 10 spare M4 x 10 cap head st sil screw 5313019 10 spare M3 st stl nut 5321004 10 spare M3 plain washer 5331005 10 spare M4 plain washer 5331006 10 spare 6 mm OD x 4 mm ID Teflon tube 6060719 3 meters spare 9 5 mm hosetail 6070120 1 spare Unex D17 hoseclip 6366317 1 spare fan filter kit 7990720 1 spare Thermo 2uest Finnigan AQA Hardware Manual 8 5 TTE Page Search Manuals Feedback web Consumables and Spares Spares FINNIGAN AG 8 6 Finnigan AQA Hardware Manual Thermo 2uest
2. Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Thermo 2uest Shutting Down and Restarting the System Restarting the System System Start up Procedure To start up the system do the following 1 Activate the LC and its associated hardware following the instructions provided by the manufacturer Wait for the LC to complete its initialization before continuing 2 Plugin the Finnigan AQA and switch it on at the mains Toggle the ON switch located at the rear of the instrument Note The Finnigan AQA vacuum pumps will not start straight away Refer to the topic Pumping down the Finnigan AQA for information on starting the vacuum pumps 4 Switch on the PC Wait until Windows is running and then start Xcalibur 6 Start the water chiller only applies if this option is fitted to your system Pumping Down the Finnigan AQA Pumping down is necessary in order to create a high vacuum within the system To pump down the Finnigan AQA right click on the Finnigan AQA server in the Windows Taskbar and choose Vacuum Pump Reaching high vacuum takes approximately 5 minutes If the Finnigan AQA has not reached vacuum after 10 minutes check for leaks in the system See the Troubleshooting chapter for advice When the Finnigan AQA has reached vacuum Xcalibur switches the server s green vacuum light on You can also monitor the vacuum status of the instrument by observing the vent and vacuu
3. Variable retention Pumping fluctuations Check the pump for problems refer to gradient analyses times the manual supplied with your pumping instrumentation Column temperature Place the column in a constant fluctuations temperature oven Rising falling Possible contamination Replace the solvents with fresh solvents baselines especially when running If necessary clean the pumping lines to remove the contamination Overly wide peaks Column degradation or pumping problems The column is overloaded Replace the chromatographic column or wash with a high percentage of a strong eluting solvent Check the performance of the pumping system refer to the manual supplied with your pumping instrumentation Reduce the injection volume and or the sample concentration The peaks have flat tops The signal exceeds the dynamic range of the detector The sample is too concentrated Reduce the detector voltage Dilute the sample Peaks tailing or fronting Column degradation or incorrect column type for the intended analysis Column overloading Replace the column or use an alternative column type stationary phase Reduce the concentration of the sample or inject less onto the column Thermo 2uest Finnigan AQA Hardware Manual 6 11 Troubleshooting Troubleshooting Tables Manuals Page Search Manuals Feedback Web FINNIGAN AQA Symp
4. Manuais Page Search Manuals Feedback Web _ FINNIGAN AQA phosphates 1 1 3 4 phosphoric acid use 3 5 use Caution 3 5 photomultiplier tube 1 29 polarity switching 1 21 power failure 6 3 power supply requirements 6 19 probe alignment procedure 6 10 alignment procedure figure 6 10 cleaning 5 20 cleaning Warning 5 20 orthogonal 1 3 Processing Setup 1 32 profile description 1 36 proteins 1 21 pumping down 1 33 7 5 Q quadrupole mass analyzer 1 29 Qual Browser 1 32 Quan Browser 1 32 R raw data figure 1 34 introduction 1 33 types of 1 33 types of raw data 1 34 viewing raw data 1 33 Rayleigh limit 1 11 rear panel fan filters cleaning 5 25 cleaning Note 5 26 position figure 5 25 troubleshooting 6 3 rebooting the PC 6 19 removal APCI 2 2 ESI 2 6 resolution troubleshooting MS problems 6 18 troubleshooting MS problems table 6 18 restarting the system 7 4 reverse phase solvents 3 3 RF lens See hexapole RF lens rotary pump adding oil 5 22 adding oil Warning 5 22 changing the oil 5 23 changing the oil Note 5 23 changing the oil Warning 5 5 5 23 checking the oil color 5 21 checking the oil level 5 21 figure 5 24 lifting Warning 5 23 maintenance 5 21 maintenance Note 5 21 replacing the foreline trap pellets 5 24 troubleshooting 6 3 6 4 S salbutamol ESI mass spectrum figure 1 11 source fragmentation figure 1 19
5. TTE Page Search Manuals Feedback web Routine and Preventive Maintenance The Hexapole RF Lens FINNIGAN AQA source flange differential aperture plate source flange stud nuts Figure 5 17 Separating the hexapole from the source flange 2 Separate the hexapole from the source flange Remove the three screws P N 5311016 securing the differential aperture plate in position and separate the differential aperture plate from the hexapole Totally immerse the hexapole and differential aperture plate in separate measuring cylinders or beakers of 50 50 methanol water and sonicate Figure 5 18 Cleaning the hexapole Caution To prevent the hexapole or the differential aperture plate from touching the bottom of the vessel and hence becoming damaged either suspend each one on a wire or place a tissue at the bottom of the vessel Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web Routine and Preventive Maintenance FINNIGAN AQA The Hexapole RF Lena 5 If necessary clean the differential aperture plate with a cotton bud Q tip soaked in 50 50 methanol water Rinse both the hexapole and differential aperture plate with methanol Dry the hexapole and differential aperture plate with nitrogen gas Assembling the RF Hexapole 1 Secure the differential aperture plate onto the hexapole using the three screws P N 5311016 2 Depress the hexa
6. USER I O PC LINK ROTARY PUMP 6A MAX SUPPLY INLET WATER AQA ae O n oO SOURCE BACKING EXHAUST RATING C C Com UT d t Figure 5 21 Rear of the Finnigan AQA showing the position of the two fans Finnigan AQA Hardware Manual 5 25 Manuals Page Search Manuals Feedback Web Routine and Preventive Maintenance The Rear Panel Fan Filters FINNIGAN AQ The filter a piece of metal gauze is held in place by a plastic screen 1 Remove the plastic screen by pulling it away from the Finnigan AQA It will snap out of place quite easily 2 Remove the gauze from the fan or screen Clean the gauze using a vacuum cleaner or blowing with compressed air The gauze can also be washed using soap and water and then air dried 4 Replace the gauze over the fan and snap the screen back into place Note Clean the gauze away from the Finnigan AQA to ensure that the dust removed from the gauze does not affect any part of the instrument 5 26 Finnigan AQA Hardware Manual ThermoC2uest Manuais Page Search Manuals Feedback Web _ Chapter 6 Troubleshooting ThermoC2uest Finnigan AQA Hardware Manual 6 i TTE Page Search Manuals Feedback web Troubleshooting Contents FINNIGAN AQa 6 ii Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Troubleshooting Int
7. Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Index A acetic acid 1 1 3 3 acetonitrile 3 3 acidic compounds 1 13 acquisition modes Full Scan 1 35 raw data types 1 34 SIM 1 38 additives summary of use table 3 6 adducts 1 13 ammonium acetate 3 4 ammonium formate 3 4 ammonium hydroxide 3 3 analog UV chromatogram 1 33 analyzer and detector schematic figure 1 29 animations 2 1 3 7 4 3 5 1 APCI applications 1 23 comparison with ESI table 1 24 flow rate 1 17 introduction 1 15 ion generation 1 15 removal 2 2 setup 2 8 source figure 1 16 source description 1 16 APCI insert figure 2 8 installing 2 8 API 1 1 applications APCI 1 23 API 1 22 ESI 1 23 AQA flow components figure 1 26 dispersion of involatiles figure 1 25 functional description 1 26 introduction 1 25 3 i setup 3 7 solvent Note 1 26 3 7 atmospheric pressure chemical ionization See APCI atmospheric pressure ionization See API B base peak chromatogram 1 33 basic compounds 1 13 bubbles in HPLC systems troubleshooting 6 22 Thermo 2uest C calibration calibration problems 6 14 calibration problems table 6 14 capillary AQA flow 3 9 ESI insert capillary 1 12 sample infusion 4 4 carboxylic acid 1 21 Cautions cleaning hexapole RF lens 5 18 cleaning the source block 5 13 cleaning the source block o rings 5 13 entrance cone 5 1
8. 6 14 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web Troubleshooting FINNIGAN AQ Troubleshooting Tables Note In the event of any problems during calibration use the Finnigan AQA tuning diagnostics facilities to obtain further information See page b 20 for details Tuning Problems able 6 6 details for each tuning problem the symptom probable cause and remedy Table 6 6 Troubleshooting tuning problems Symptom Probable cause Remedy Delayed response to Dirty charging source Clean the source block hexapole RF changes in tuning block hexapole RF lens lens Refer to the topics The Source parameters Block and The Hexapole RF Lens in the chapter Routine and Preventative Maintenance No response to Faulty source electrical Check the connections and reconnect if changes in tuning connections necessary parameters Faulty electronics check the Please call your local ThermoQuest Tune window readbacks and Service Representative with any run the diagnostic tests diagnostic test results Low or no signal Refer to Low Sensitivity Refer to Low Sensitivity Problems on Problems on page page 6 5 Faulty source electrical Check connections and reconnect if connections necessary See and Figure 6 3 Faulty electronics Check the Tune window readbacks Run the instrument diagnostic tests Call your local ThermoQuest Service Representative
9. Manuals Page Search Manuals Feedback Web _ QD Thermo 2uest Finnigan AQA Including Navigator with aQa Hardware Manual Revision C FM101638 TIE Page Search NETS TESTES Feedback Xcalibur and AQA are trademarks of ThermoQuest Corporation Eppendorf is a registered trademark of Eppendorf Netheler Hinz GmbH Microsoft and Windows NT are registered trademarks of Microsoft Corporation PEEK is a trademark of Victrex plc Rheodyne is a registered trademark of Rheodyne Inc Swagelok is a registered trademark of Swagelok Corporation Teflon is a registered trademarks of E I DuPont DeNemours and Co Tygon is a registered trademark of Norton Industrial Plastics Valco is a registered trademark of VICI Valco Instruments Co Inc Technical information contained in this publication is for reference purposes only and is subject to change without notice Every effort has been made to supply complete and accurate information however ThermoQuest Corporation assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this manual or the information contained therein even if this information is properly followed and problems still arise This publication is not part of the Agreement of Sale between ThermoQuest Corporation and the purchaser of ThermoQuest system In the event of any conflict between the provisions of this document and tho
10. Thermo 2uest Finnigan AQA Hardware Manual 5 11 TTA Page Search Manuals Feedback web Routine and Preventive Maintenance The Source Block FINNIGAN AQa 4 Remove the two entrance cone screws P N 5311023 the entrance cone P N 9227 5 and the entrance cone o ring P N FM100231 entrance cone o ring Figure 5 10 Removing the source entrance cone Caution Exercise great care when handling the entrance cone Always store with the cone facing upwards 5 12 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web Routine and Preventive Maintenance FINNIGAN AQA The Source Block 5 Remove the two exit cone screws P N 5314015 and the exit cone P N 9227 3 exit cone Figure 5 11 Removing the source exit cone 6 Sonicate the disassembled component parts except the o rings first in a 196 v v solution of formic acid then in water and then in methanol Caution Ensure that the parts do not become damaged in this process If necessary sonicate each part separately In particular ensure that the cones are face up at all times Caution Do not sonicate the o rings as the solvent and acid may damage them Thermo 2uest Finnigan AQA Hardware Manual 5 13 TE Page Search Manuals Feedback web Routine and Preventive Maintenance The Hexapole RF Lens FINNIGAN AG 5 5 The Hexapole RF Lens The hexapole RF lens can be removed from the
11. 1 13 source description 1 12 ESI ceramic gas nozzle cleaning 5 3 orientation figure 2 5 ESI insert figure 2 3 5 4 installing 2 3 F fan filters See rear panel fan filters Finnigan AQA analyzer and detector schematic figure 1 29 APCI source figure 1 16 components figure 1 2 ESI source figure 1 13 exterior features 1 5 front view figure 1 5 front view doors open figure 1 7 introduction 1 1 power supply requirements 6 19 rear view figure 1 8 schematic figure 1 3 source schematic figure 1 10 status light panel figure 1 5 System overwiew 1 2 Finnigan AQA Properties dialog box figure 1 33 flow rate APCI 1 17 columns 3 2 columns table 3 2 ESI 1 14 flow splitting accuracy Note 3 13 procedure 3 12 schematic figure 3 12 2 Finnigan AQA Hardware Manual foreline trap pellets replacing 5 24 replacing Warning 5 24 troubleshooting 6 4 formic acid 1 1 3 3 fragment ions 1 18 Full Scan mode centroid 1 35 centrold figure 1 35 introduction 1 35 MCA 1 37 MCA figure 1 37 profile 1 36 profile figure 1 36 G gas nozzle orientation figure 2 5 glucuronide metabolites 1 21 graph AQA flow rate against reservoir pressure 3 11 sample infusion rate against reservoir pressure 4 6 H heater wires and thermocouple moving the probe Caution 5 16 hexapole RF lens assembling 5 19 assembly Note 5 19 cleaning Caution 5 18 cleaning Warning
12. 5 14 cleaning procedure 5 14 disassembling and cleaning 5 17 disassembly Note 5 17 overview 1 29 removing 5 14 removing Note 5 14 Home Page 1 31 horse heart myoglobin mass spectrum figure 1 20 HPLC bubble problems and degassing 6 22 buffers and additives 6 22 contamination 6 23 injection valves 6 25 mobile phase reservoir 6 22 preventative maintenance and spares 6 27 troubleshooting 6 22 tubing and fittings 6 23 use of solvents and additives with Finnigan AQA 3 3 UV detectors 6 25 Thermo 2uest FINNIGAN AQA Manuais Page Search Manuals Feedback web _ Index I infusion system See sample infusion system injectors LC 6 25 inlet system chromatography problems 6 11 problems table 6 11 inorganic acids 3 5 insert APCI 2 8 APCI figure 2 8 cleaning ESI insert 5 3 ESI 2 3 ESI figure 2 3 5 4 flushing 5 3 flushing Note 5 3 handling Caution 2 2 2 7 2 8 replacing 5 5 Instrument Setup 1 32 ion evaporation 1 11 ion generation APCI 1 15 APCI figure 1 15 ESI 1 11 ESI figure 1 11 ion pairing agents 1 1 3 4 ionization modes APCI 1 15 changing 2 i ESI 1 10 K kit consumables 8 2 Source o rings 8 3 Source screws and fixings 8 4 L LC MS considerations 3 2 flow rate 3 2 flow rate table 3 2 introduction to AQA 1 1 Library Browser 1 32 low sensitivity problems 6 5 problems table 6 5 M m z 1 4 maintenance s
13. Troubleshooting Tables Symptom Probable cause Remedy Weak signal continued Blocked ESI APCI insert Replace the insert Refer to the chapter Changing lonization Modes Damaged ESI APCI insert Replace the insert Refer to the chapter Changing lonization Modes Incorrect probe temperature Check instrument method and Tune window values for the probe temperature Check probe temperature readback in the Tune window If incorrect check the integrity of the two thermocouple and two heater connections to the probe If any of the connections are damaged call your local ThermoQuest service representative Incorrect source voltage Infuse the sample into the source and optimize the source voltage to give the maximum signal No source voltage the readback in the Tune window is zero a region see Figure 6 1 and 6 2 Check all electrical connections in the Call your local ThermoQuest Service Representative if this does not remedy the problem Damaged ESI ceramic jet insulator Replace the part Refer to the topic Cleaning the ESI Insert and Ceramic Gas Nozzle in the chapter Routine and Preventative Maintenance Incorrect APCI corona discharge pin position Check that the corona discharge pin is positioned correctly Refer to the chapter Changing lonization Modes Dirty APCI corona discharge pin Clean the corona discharge pin using a very fine abrasiv
14. Vacuum leak Vent the instrument and check all source o rings for signs of damage Replace as necessary Refer to the topic The Source Block in the chapter Routine and Preventative Maintenance Weak signal Poor or incorrect sample Prepare fresh samples preparation Excessive condensation in the Dry the inside of the source enclosure source enclosure Ensure that the probe temperature is high enough for the flow rate and that the source enclosure is hot before starting the liquid flow The ESI Probe kV readback Check for excessive condensation in the voltage is lower than the set source enclosure Dry if appropriate voltage Faulty electrical source Check the source voltage connection and connection reconnect if appropriate see Figure 6 2 Dirty hexapole RF lens Check for abnormal tuning conditions for assembly the RF Lens and or ion energy If applicable thoroughly clean the hexapole RF lens assembly see the topic Cleaning the Hexapole RF lens in the chapter Routine and Preventative Maintenance Note that contamination on the hexapole RF lens will only build up over a period of time and cannot account for a sudden loss in sensitivity Incorrect detector voltage Check that the voltage setting on the detector is correct Increase the value if necessary typical value is 650 V 6 6 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Troubleshooting
15. crystallize in the source block the entrance cone and prevent the mass spectrometer from functioning The most common non volatile salts used are phosphates e Ion pairing agents Ensure that AQA flow is running when using ion pairing agents for example sodium octanesulfonic acid Many ion pairing agents suppress electrospray ionization Least Suitable Additives Least suitable additives are surface active agents detergents These can suppress the ionization of other compounds Detergents by their very nature are concentrated at the surface of a liquid This causes problems with electrospray as the ionization relies on the evaporation of ions from the surface of a droplet The detergent therefore suppresses the evaporation of other ions Use surfactants only when they are being analyzed themselves not as additives to HPLC mobile phases Other Solvents Other solvents are e Normal phase solvents Normal phase solvents such as dichloromethane hexane and toluene are most suitable for use in APCI e Propan 2 ol IPA 2 methoxyethanol ethanol and so on These have all been used with LC MS but their use tends to be application specific e Dimethyl sulfoxide DMSO This solvent is commonly used by synthetic chemists for primary dilution Finnigan AQA Hardware Manual Thermof 2uest Manuals Page Search Manuals Feedback Web _ LC MS and AQA Flow FINNIGAN AQA LC MS Considerations Other Additives
16. mounted between the heated region and the entrance cone ionizes the sample molecules with a discharge voltage of approximately 3 0 to 3 5 kV in positive ion mode and 2 0 to 3 0 kV in negative ion mode High Vacuum Region Exit cone Intermediate Rotary Pressure pump Region Flow Flow disrupter pin focusing region Entrance cone Z Kon flow Probe 7 Ed Atmospheric een Pressure NS Region LC eluent 4 ey Nebulizing gas N Corona pin Sheath gas N Figure 1 13 Schematic of the AQA APCI source on the Finnigan AQA showing the principal components and pressure regions The newly formed ions then enter the flow focusing region through the entrance orifice and pass into the RF lens region The RF lens hexapole helps to focus the ions before they enter the mass analyzer region Note The source chamber flow disrupter pin and cones are all at the same electric potential which forms a field free region within the source Finnigan AQA Hardware Manual ThermoC2uest Manuais Page Search Manuals Feedback Web FINNIGAN AQA ThermoC2uest Introducing the Finnigan AQA The Source an Introduction to API Techniques Spectral Characteristics Like electrospray APCI is a soft ionization technique and forms singly charged ions either the protonated M H or deprotonated M H molecule depending on the selected ionization mode Unlike electrospray however APCI does not produce
17. 1 apply Table 3 1 LC columns and flow rates Column ID Flow rate omm o O capitay o 1 0 mm 40 50 uL min capillary lt 10 uL min The ionization mode determines the flow rate and hence column ID that is used The following guidelines apply e Electrospray on the Finnigan AQA can operate at all the flow rates described in Table 3 1 and hence the full range of column IDs can be used without splitting the flow e APCIcannot operate at flow rates below 0 2 mL min therefore suitable column IDs are 2 1 mm 3 9 mm and 4 6 mm Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Thermo 2uest LC MS and AQA Flow LC MS Considerations HPLC Solvents and Mobile Phase Additives The following section is a guide for the choice of solvent and mobile phase additives The choice of solvents for LC will be dictated primarily by the separation requirements but there are some guidelines that need to be followed These take the form of selected examples which have been divided into three categories most compatible least suitable and other less common ones In all cases degassed solvents are necessary for LC MS operation Sonication helium sparging or vacuum membrane degassing achieves this Helium sparging and vacuum membrane degassing are the more efficient techniques Most Compatible Solvents Most compatible solvents are e Water e Acetonitrile e Met
18. 1100 1200 1300 Figure 1 15 Electrospray spectrum of horse heart myoglobin This envelope is represented in diagrammatic form in The first diagram shows the envelope at a source voltage of 30 V Next the envelope is shown at 60 V There is no ramping applied here The envelope has the same shape but has moved to a higher m z value This is due to the charge stripping that occurs at high source voltages which lowers the charge state and produces an apparent higher mass distribution If the source voltage is ramped between 30 and 60 V the charge distribution envelope is extended and it resembles the lower diagram Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web Introducing the Finnigan AQA FINNIGAN AQa The Source an Introduction to API Techniques Intensity Intensit Without source voltage ramping bs dd Without source voltage ramping Source voltage 30V Source voltage 60V Increasing number of charges Decreasing number of charges m z m z Intensity With source voltage ramping 30 60V AN Figure 1 16 Source voltage ramping Source voltage ramping is often used for proteins and peptides during e Calibration to extend the calibration range e Analysis to increase the number of charge states leading to greater accuracy of molecular weight determination Note Source voltage ramping will not perform source fragmentation because the
19. 24 stainless steel 6 24 Teflon 6 23 use of stainless steel tubing Warning 6 24 tune diagnostics dialog box figure 6 20 running 6 20 running Note 6 21 tune diagnostics completed figure 6 21 tuning tuning problems 6 15 tuning problems table 6 15 U UV detectors 6 25 V vacuum Finnigan AQA under vacuum Note 7 2 pumping down 7 5 starting vacuum pumps Note 7 5 troubleshooting vacuum problems 6 17 troubleshooting vacuum problems table 6 17 vacuum system introduction 1 30 troubleshooting 6 3 6 4 vent 1 33 volatile buffer systems 1 1 W Warnings adding rotary pump oil 5 22 changing ionization modes 2 2 2 3 2 6 2 8 changing the rotary pump oil 5 23 hexapole RF lens cleaning 5 14 lifting rotary pump 5 23 probe cleaning 5 20 replacing foreline trap pellets 5 24 source block cleaning 5 6 use of stainless steel tubing 6 24 using concentrated nitric acid 5 5 water 3 3 X Xcalibur Home Page 1 31 Home Page figure 1 31 introduction 1 31 rebooting the PC 6 19 server 1 32 server figure 1 32
20. 4 ii Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA AQA Sample Infusion System Introduction ThermoC2uest 4 1 Introduction The Finnigan AQA s built in sample infusion system allows easy calibration and tuning This chapter provides instructions on how to setup the AQA sample infusion system Finnigan AQA Hardware Manual 4 1 TTE Page Search Manuals Feedback web AQA Sample Infusion System Overview FINNIGAN AQa 4 2 Overview The recommended way to introduce a sample for tuning and mass calibration is to use the AQA sample infusion system This method provides a steady flow of sample directly into the source typically at flow rates of 50 uL min Direct sample infusion is used to introduce the following e Calibration sample e Sensitivity verification sample e Compound of interest for tuning Note Due to the low flow rates involved direct sample infusion is normally used only with electrospray In APCI a sample can be infused into the source using a splitter see Figure 4 1 Infuse the sample into a suitable LC flow for example 0 5 mL min via the splitter before the sample enters the source AQA reservoir LC pump To the APCI insert and source zero dead volume T piece Figure 4 1 Using a splitter to add a suitable LC flow to the sample infusion flow for operation in APCI 4 2 Finnigan
21. 5 2 5 3 The Electrospray and APCI Inserts sicoqenve cobeent cete cui eph ot Cub eq eto vL cp o Set Eee cta Peor cR reisse 5 3 lushitig the Inserts Eon cte ER erii ord Hic fe redet ovas 5 3 Cleaning the ESI Insert and Ceramic Gas Nozzle eee 5 3 Replacing the Inserts 1 rone yt Esteri Er Raya detur od OR be eee ep ai per eg a ege eva eeu 5 5 ii Finnigan AQA Hardware Manual ThermoC2uest Manuais Page Search Manuals Feedback Web FINNIGAN ACA Contents 5 4 Whe Source BOCK mr 5 6 Cleaning the Entrance Cone eterne teer eerte Feet kat nne erp Etape Sua SE e cea 5 6 Cleaning the Source Block eie ice tec etre eter ode ceo d rds 5 7 2 Th Hexapole RF Lets aueosscuse t repito den MR NE ENERSUT CUP NTC E EI UR UN GUB RD HUNE UE 5 14 Cleaning the Hexapole RF Lens esses eene enne nennen innia 5 14 56 dvo MER rcc ER EN 5 20 57 The Rotary PON ven saruistksuiedbsacindieibisus ben e e asd isti tpe Caes i mo vti Ei anus 5 21 Checking the Rotary Pump Oil Level and Color eene 5 21 Changing the Rotary Pump Oil esses enne rennen nennen 5 23 Replacing the Foreline Trap Pellets eee enne 5 24 5 8 Th Rear Panel Fan Filters sia scie codon ocium n Oi alcol deine e ib cond uii buses co FERE Leodii ete 5 25 flush D A 6 i SEME
22. 6 11 2 66 NL D0 249E5 Il 7 I TIC carb o 80 i mix pmix03 o J l s e 282 5 EN 3 lt BER o B 404 BI AE 235 328 9 g a 55 223 j A JME 387 4B 475 5g 532 542 20 pe CN EO Se Oe 15 2 0 25 3 0 35 40 45 50 55 60 Time min carb mix pmix03 102 RT 2 66 AV 1 SB 38 1 42 2 07 2 87 3 15 NL 1 02E5 T c ESI Full ms 150 00 500 00 281 2 1005 2 a e 807 oO E S 604 g 607 lt x J L 40 ie 459 1 E 240 3 207 J 282 5 454 1 i 181 5 2294 256 2 346 8 387 0 403 2 1 461 0 482 1 150 200 250 300 350 400 450 500 m z Figure 1 25 A mass spectrum taken at retention time 2 66 minutes lower trace from a TIC chromatogram upper trace Raw Data Types The data can be collected and stored by the data system in two different ways Full Scan and Selected Ion Monitoring SIM The main difference between these two modes is e In Full Scan mode data is collected across the whole scan range e In SIM mode data is acquired only at specific mass to charge ratios 1 34 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN ACXA ThermoC2uest Introducing the Finnigan AQA The Data System Full Scan Mode There are three different types of Full Scan acquisition These are e Centroid e Profile e MCA Multi Channel Analysis In all full scan acquisitions raw data is collected over the whole scan range defined
23. AQA Figure 1 6 is a schematic of the rear view of the Finnigan AQA ee ee Contact closure Ed COM 1 COM2 loai a ed USER I O PC LINK analog inputs PEL To PC ROTARY PUMP WATER AQA 6A MAX SUPPLY INLET D E INLET SOURCE BACKING EXHAUST Q voy ueBiuun YN A ad INLET RATING Torrotary Gas inlet to Power To rotary pressurize switch inlet via pump inlet AQA reservoir foreline Navigator puni power tra Gas inlet for Rotary pump e AER nebulizer and power rom sheath gas source To and from water chiller Figure 1 6 Rear view of the Finnigan AQA 1 8 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA Thermo 2uest Introducing the Finnigan AQA The Source an Introduction to API Techniques 1 3 The Source an Introduction to API Techniques The source or interface performs four main functions e Separates the analytes from the solvent and buffer systems used in LC e Jonizes the analyte molecules e Allows efficient transfer of ions into the mass analyzer for detection LC eluent enters the source through the orthogonal sample introduction probe The primary objective of an orthogonal probe is to direct any involatile components present in the LC eluent such as those from buffers ion pairing agents or matrices away from the entrance orifi
24. AQA Flow describes how to set up AQA flow It describes the LC MS factors to be taken into account when using Finnigan AQA Chapter 4 AQA Sample Infusion System describes how to set up the AQA sample infusion system Chapter 5 Routine and Preventive Maintenance provides details of the maintenance tasks which must be performed to keep the Finnigan AQA in optimum condition Chapter 6 Troubleshooting helps you to diagnose and resolve problems that may occur from time to time with the Finnigan AQA Chapter 7 Shutting down and Restarting the System describes how to shut down the system for both short and long periods It also describes how to restart the system following a long term shut down Chapter 8 Consumables and Spares lists the parts that may be necessary in the course of working with and maintaining the Finnigan AQA MS detector Finnigan AQA Hardware Manual V TTE Page Search Manuals Feedback web Read This First Changes to the Manual and Online Help FINNIGAN AG vi Changes to the Manual and Online Help To suggest changes to this manual or the online Help please send your comments to Technical Publications Manager ThermoQuest Crewe Road Wythenshawe Manchester M23 9BE UK You are encouraged to report errors or omissions in the text or index Thank you Finnigan AQA Hardware Manual Thermof 2uest Manuais Page Search Manuals Feedback Web FINNIGAN AQA ThermoC
25. Feedback web Routine and Preventive Maintenance The Source Block FINNIGAN aQu 5 4 The Source Block The source block can be removed from the instrument see page 5 7 and disassembled see page into its component parts for cleaning Typically the entrance cone needs to be cleaned most frequently because it becomes dirty with use over a long period The cone can be reached without the need to remove the source block from the instrument WARNING Allow the source block and probe heater assembly to cool before carrying out any maintenance Cleaning the Entrance Cone 1 Vent the instrument if it is currently under vacuum Right click on the server and choose Vacuum Vent 2 Expose the entrance cone Retract the corona pin if in APCI mode or remove the ESI ceramic gas nozzle and insert if in ESI mode and move the AQA capillary support away probe corona pin AQA capillary support Figure 5 4 Exposing the source entrance cone 3 Remove the entrance cone after venting and sonicate first in a 1096 v v solution of formic acid and then in methanol 5 6 Finnigan AQA Hardware Manual ThermoC2uest TA Page Search Manuals Feedback web Routine and Preventive Maintenance FINNIGAN AQA The Source Block Cleaning the Source Block It is good practice to clean the entire source on a weekly basis particularly if complex sample matrices or chromatographic buffers are routinely used Carry out t
26. Flow FINNIGAN AG 1 26 Functional Description As shown in Figure 1 19 AQA flow consists of a pressurized reservoir filled with solvent typically HPLC grade water or organic solvents such as methanol and a fused silica capillary One end of the capillary is inserted into the reservoir while the other end is fed to the edge of the inlet orifice of the entrance cone When the pressure in the AQA reservoir is increased the solvent is forced through the fused silica capillary and delivered to the edge of the inlet orifice The pressure in the reservoir can be controlled and hence the flow rate of the solvent fused silica capillary entrance cone AQA reservoir Figure 1 19 The components of the solvent delivery system Note It is necessary to use the AQA flow system only for compounds in dirty matrices or when involatile buffers are used Choose the AQA solvent to give the most effective solubility for the expected contaminants Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web FINNIGAN AQA Thermo 2uest Introducing the Finnigan AQA The Sample Infusion System 1 5 The Sample Infusion System This section introduces the AQA sample infusion system Information on how to set up the sample infusion system is given in the chapter AQA Sample Infusion System Introduction The recommended way to introduce a sample for tuning and mass calibration in ele
27. Getting Started manual for details If any of the peaks have an ion count of greater than 2x106 reduce the concentration of the sample or reduce the detector voltage Spectra show high acetonitrile adduct formation The source gases flow rate is too low Vacuum leak Dirty hexapole RF lens Some samples have a high tendency to from acetonitrile adducts Check that the cylinder pressure is set correctly Check for leaks in the supply lines Check that the insert is correctly fitted Vent the instrument and check all source and hexapole o rings for signs of damage Replace as necessary Refer to the topics The Source Block and The Hexapole RF Lens in the chapter Routine and Preventative Maintenance Clean the hexapole RF lens Refer to the topic The Hexapole RF Lens in the chapter Routine and Preventative Maintenance If problems are still encountered contact your local ThermoQuest Service Representative Use methanol rather than acetonitrile if possible Thermo 2uest Finnigan AQA Hardware Manual 6 13 Manuals Page Search Manuals Feedback Web _ Troubleshooting Troubleshooting Tables FINNIGAN AQA Calibration Problems able 6 5 details for each calibration problem the symptom probable cause and remedy Table 6 5 Troubleshooting calibration problems Symptom Probable cause Remedy The Instrument does not calibrate Refer to Low Sensi
28. Page Search Manuals Feedback Web FINNIGAN AQA Thermo 2uest Introducing the Finnigan AQA The Source an Introduction to API Techniques e Source fragmentation is used in both APCI and electrospray to give structural information In general increasing the voltage applied to the source block the source voltage yields increasing amounts of fragmentation depending on the nature of the compound The optimum source voltage required to give the maximum intensity of the protonated or deprotonated molecule is compound dependent as is the source voltage required for fragmentation The energies involved in source fragmentation are low so usually only weaker bonds such as C N and C O are broken Since there are many similarities between electrospray and APCI there are many applications common to both Compounds suitable for analysis by electrospray are polar and of molecular weight less than 100 000 amu The higher molecular weight compounds such as proteins can produce multiply charged ions As it is the mass to charge ratio m z that is measured by the MS detector these can often be seen at lower masses For example if the molecular weight is 10 000 a doubly charged ion 2 in ve ion would be seen at m z 5001 10 at m z 1001 etc Typical electrospray applications are peptides proteins oligonucleotides sugars drugs steroids and pesticides Compounds suitable for analysis by APCI are generally polar although l
29. Peaks shifted from Poor calibration Re calibrate Refer to the Finnigan AQA their nominal mass Getting Started manual for details position Note In the event of any problems during tuning use the Finnigan AQA tuning diagnostics facilities to obtain further information See page 5 20 for details Thermo 2uest Finnigan AQA Hardware Manual 6 15 Manuals Page Search Manuals Feedback Web _ Troubleshooting Troubleshooting Tables FINNIGAN AQA Communication Problems able 6 7 details for each communication problem the symptom probable cause and remedy Table 6 7 Troubleshooting communication problems Symptom Probable cause Remedy No communication with the other equipment Loose or incorrectly inserted cables PC system crash Unsupported communications Incorrect firmware version Waters Alliance only A transient break or fluctuation in mains power supply has halted Xcalibur A malfunction has occurred in the MS or LC system electronics Check all the cables from the Finnigan AQA the PC and the LC system Refer to the Finnigan AQA Getting Connected manual Reboot the PC if necessary Refer to the topic Rebooting the PC on page le 19 tor details Reboot the PC Use contact closure to start the MS detector Obtain a firmware upgrade or use contact closure to start the MS detector Reboot the PC Contact your local ThermoQuest servi
30. The vacuum system consists of two types of vacuum pumps two turbomolecular pumps and one rotary pump The turbomolecular pumps are housed within the Finnigan AQA and must be serviced only by a trained service engineer The rotary pump is external to the Finnigan AQA and requires routine maintenance to keep it running at its optimum performance level The following maintenance procedures are covered here e Checking the rotary pump oil level and color e Adding oil to top up the oil level e Changing the rotary pump oil e Replacing the foreline trap pellets Note More information on operating and maintaining the rotary pump can be found in the Rotary Pump User Manual supplied with the Finnigan AQA system Checking the Rotary Pump Oil Level and Color Check the rotary pump oil level and color at least once a week If the oil level in the rotary pump gets low before the scheduled oil change use the procedure in the next section to add oil To check the oil 1 Look through the viewing window at one end of the rotary pump The oil level should be between the upper and lower marks positioned next to the window 2 Add more oil if the oil level is near or below the lower mark Refer to the procedure for adding oil on page If a six monthly service is due it may be more convenient to drain and replace the oil In this case refer to the procedure for changing the rotary pump oil on page 5 23 If the oil has turned red in color
31. There are two occasions when the instrument should not be totally shut down but left in a stand by mode These are as follows e Between analytical runs e For any other period up to two weeks For periods of longer than two weeks the instrument should be fully shut down In Between Analytical Runs Between analytical runs turn the API gas flow off to conserve the supply Follow the steps described below 1 Open the Finnigan AQA Tune window a Click on Instrument Setup on the Home Page Road Map view b Click on the Finnigan AQA button c Click on the Analysis tab to display the Analysis page d Click on the Tune button 2 Choose Instrument Gas or click on the Toggle Gas toolbar button to switch the nitrogen gas flow Off Up to Two Weeks For periods of up to two weeks first follow the steps described above and then do the following 1 In the Finnigan AQA Tune window choose Instrument Operate or click on the Toggle Operate toolbar button to switch Operate Off 2 Switch off the PC monitor Leave the remainder of the system running with the Finnigan AQA under vacuum Note Leave the Finnigan AQA under vacuum during the switching of ionization modes and basic maintenance procedures It is good working practice not to vent the instrument unless non routine maintenance is being carried out Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web FINNIGAN
32. by the start and end mass Centroid During centroid acquisitions Xcalibur automatically determines and saves the mass center of the acquired profile peak returned from the detector Hence the previously large number of points that described the mass spectral peak are reduced to a single centroid stick see for each ion mass recorded This has the advantage of reducing the quantity of data recorded to the hard disk and improving processing speeds 120 140 160 180 200 220 240 260 280 Figure 1 26 Full scan centroid spectrum of pentachlorophenol Finnigan AQA Hardware Manual 1 35 Introducing the Finnigan AQA The Data System FINNIGAN AQA 1 36 Profile With profile acquisition data is not centroided into sticks Instead the signal received by the interface electronics is stored to give an analog intensity profile of the data being acquired for every scan see Figure 17 Profile acquisition enables mass spectral peak width and resolution to be examined and measured For example the resolution between an ion and its isotope s or multiply charged ions can be seen and measured if necessary This is most useful in the case of protein and peptide analysis where multiply charged ions are formed Due to the fact that data is being written to disk at all times even when there are no peaks being acquired profile data acquisition places an extra burden on the acquisition system in comparison to centroi
33. clockwise to pressurize the AQA reservoir When the regulator reads approximately 12 psig stop turning and push the adjuster into its locked position A reservoir pressure of approximately 12 psig is needed to produce the desired AQA flow rate of 40 uL min Figure 3 5 Turning the mini regulator adjuster The graph in Figure 3 6 shows the relationship between the pressure within the AQA reservoir and the AQA flow rate onto the entrance cone 80 puts ues TERN ME VENE CS MEE qoe se gres qp Sape es rere i j 70 4 4 7 EEE potete tum jos Es eere fe a quocp Mercer 1 p l 1 c 604 pepe pepe emp PAS a p pem E I l I S n 1 5U0 4 4 adaa ee n SES ie ddan ka daia bee Hee Het sae an a 40 4 b 4 H ee a t a Poco nenn goss i i f f f f l 30 L n E M oe doe 8 90 i l 50 1 rr i T eye Mie ees cower E doo tee ae Ebro corer eo Oy med G 20 j M gees eee REPE RR E s lesse Teh Te eal ees dou 10 l l 0 2 4 6 8 10 12 14 16 18 20 22 24 26 Reservoir pressure psig Figure 3 6 Graph of AQA flow rate against reservoir pressure fused silica dimensions length 450 mm ID 0 1 mm OD 0 36 mm Thermo 2uest Finnigan AQA Hardware Manual 3 11 LC MS and AQA Flow Flow Splitting FINNIGAN AQA 3 12 3 4 Flow Spli
34. corona pin a series of reactions occur that give rise to charged reagent ions Any sample molecules which elute and pass through this region of reagent ions can be ionized by the transfer of a proton to form M H or M HJ This is a form of chemical ionization hence the name of the technique Atmospheric Pressure Chemical Ionization Corona pin Heated nebuliser Solvent molecules Sample molecules 0000060000008 P Collisions and proton transfer Ne gt 1d x09 8 Liquid SN dw o e 0 e 60O up eg e N gt l Oy O o O Oe 0000000000000 2 Solvent molecules Sample An aerosol Solvent and are ionized M H is formed sample molecules ions formed are desolvated Figure 1 12 Positive ion APCI mechanism Thermo 2uest Finnigan AQA Hardware Manual 1 15 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AG APCI Using the AQA Source The sample is carried to a spray region via a 100 um ID fused silica insert capillary The action of both the nebulizing gas and the heated probe lead to the formation of an aerosol The desolvation process is assisted by a second concentric flow of nitrogen gas the sheath gas In contrast to electrospray APCI is a gas phase ionization technique Ionization occurs as the aerosol leaves the heated nebulizer region A corona pin
35. e Trifluoroacetic acid TFA This is frequently used for peptide and protein analysis High levels gt 0 1 v v can cause suppression of sensitivity in positive ion mode TFA may completely suppress ionization in negative ion mode e Triethylamine TEA This may suppress the ionization of less basic compounds in positive ion mode as it also is readily ionized to give a M H ion at m z 102 TEA enhances ionization of other compounds in negative ion mode because it is basic This is a particularly useful additive for the analysis of nucleic acids e Tetrahydrofuran THF In ESI use of THF can reduce sensitivity This effect can be counteracted by post column addition of ammonium acetate It has no effect in APCI Caution Do not use a concentration of THF greater than 5 with PEEK tubing THF causes swelling in the PEEK tubing and consequently presents a risk of the LC tubing bursting e Inorganic acids Inorganic acids for example sulfuric acid or phosphoric acid can be used Check the suitability of the LC column to low pHs Caution After using phosphoric acid thoroughly clean the source source enclosure and hexapole RF lens to minimize the physical damage Thermof 2uest Finnigan AQA Hardware Manual 3 5 Manuals Page Search Manuals Feedback Web _ LC MS and AQA Flow LC MS Considerations FINNIGAN AQa Summary of Additives Table 3 2 Summary of additive use Avoid Positive ion Trif
36. ee nas eiia ia 6 23 Tubing and Fitting e 6 23 Injection Eli m senseri an engia eni e Races dade dave APE TEER 6 25 UV IDOLE CLOTS orase e E r E EA E ESS 6 25 Preventative Maintenance and Spares sese eren nennen ren 6 27 ThermoC2uest Finnigan AQA Hardware Manual iii Manuals Page Search Manuals Feedback Web _ Contents FINNIGAN AGRA Shutting Down and Restarting the System sccsssccssssscssssscssssscssssccssssscsssssssssscsssssscnscees 7 i rs E odio m 7 1 7 2 Instrument Standby and Shutdown cccccecsecssessceseeseeeeceseeseeseceseeseeeseseecsaeeseseceaeeseeeeseeeseees 7 2 In Between Analytical Runs 21412 tior tete tete r teer anias 7 2 Up tocLwo WOeeks uere tico aS ene ert aces ee er eub eene tes eub ee ue tarea b esent ESETERE e an eT RE 7 2 Two egg E asi iabees 7 3 7 3 Restarting the System onscreen e e E eea eaa EEEE R NE 7 4 Pre switch on Checklist cscs scsctessasdvessnedsetersonccenshvassteasensddegcananscdasancesinsnasntssoeadesonsaasetsassaseds 7 4 System Start up Procedure 0 cccccecssessseceeneeceeeeeceeeeesaeceeaeeceeaeeeeaaeceeaeeceeeeeeaeeeeaeceeaeeees 7 5 Pumping Down the Finnigan AQA sees enne ener 7 5 Consumables and S PALES aues cite ec iiec R RN ERE EB VE NUR ORE ERN ERE KR EOD MEA HER V uU ERE UK ERA QE RNV AR RR QN ENS 8 i CMMEMNI DoD Re P 8 1 amp 2 Cons mables s iet
37. emissions standard for USA The products identified above comply with the EU directive 73 23 EEC by meeting the following standard EN61010 1 1993 Safety requirements for electrical equipment for measurement control and laboratory use The technical documentation is available for inspection by the relevant enforcement authorities The CE mark was first applied in 1998 Signed A i WUU Dr W E McKnight Authority Managing Director Date May 1999 ATTENTION The attention of the purchaser installer and user is drawn to the special measures and limitations to use which must be observed when the product is taken into service to maintain compliance with the above directives Details of these measures are contained in the User Manual ISO 9001 Accredited 925584 TA Page Search Manuals Feedback web Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Contents Contents IMEEM olo NR 1 1 12 System OVervVieW e cc M 1 2 What is Mass Detection eie dna iere ee epe eee E ko dives LE EET pe BEST p ebore 1 4 Exterior Features of the Finnigan AQA sse een nennen 1 5 1 3 The Source an Introduction to API Techniques erabo reri re ea ere pe vr Pu VPE POR Hid EG KR 1 9 Electrospray d eE 1 10 Atmospheric Pressure Chemical Ionization eeeeeeeeeneeneeen eene 1 15 Source Fragmentation eese
38. esses eee eene nnne enn nennen nnne entes nnne tree 1 18 Source Voltage Rampin 9 e tite tee re nene cba Er PCR Dee R ARENES 1 20 Polarity Switching iuuat eere HERE EL eL EE ep Ee sop epa be EYE ia 1 21 Application of API Techniques ces cescesceseceeeceseeeseeeeaeeeaeeeaeecaecsaecsaeeeaesaeenaeeeaeen 1 22 1 4 The Self Cleaning Source AQA PIOQ viret HEVERE HH CERE PUR E EVERE SPUREN ER Ur RESET 1 25 TiNtPOMUCHION AA P 1 25 Functional Descriptio nici uu coeno teret th e eene tg Pee Rae eaae Poe ero aep Rt edu 1 26 1 5 Th Sample nfuston Systetiiu ue vec mdi aree terae io iia aiaa uk 1 27 nngeniiuno m 1 27 Functional Description iio riesen te era Seis ae Pe uper ee Uere io oa 1 27 1 6 The Mass Analyzer and Detector acies bbb qur ek baisses sts taken pH E ua Beds tH E I M ete 1 29 1 7 Th Vaeudi Sy SEI ien sspe Noe eda re ev DURER ERU en rite Ln ied uia UR E RR bU Ae 1 30 18 TheData Syste sesiunii sioneer FR DUMP DEB GP FUE m NEEE 1 31 NIordn AIC ec M 1 31 ThermoC2uest Finnigan AQA Hardware Manual i Manuals Page Search Manuals Feedback Web _ Contents FINNIGAN ACRA RaW Data p 1 33 Raw Data Types sv iciendiciseies Lem teleewiicdaeedi dapeepsdesdrasigiiteeastelvteis dupaesteonsnetiewes beds 1 34 Changing Ionization Modes 2 i 2 B vim reena 2
39. evaporates the from the surface ions electric field increases and ions move towards the surface Figure 1 9 Positive ion electrospray mechanism Finnigan AQA Hardware Manual 1 11 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AG Electrospray lonization Using the AQA Source The sample in solution enters the source via a 75 um ID stainless steel insert capillary held at a voltage of 3 to 5 kV The insert capillary is surrounded by a tube that directs a concentric flow of nitrogen nebulizing gas past the droplets of liquid forming at the probe tip The action of the nebulizing gas high voltage and heated probe produces an aerosol of liquid droplets containing ions of the sample and solvent The ion evaporation process is assisted by a second concentric flow of nitrogen gas This is the sheath gas This highly efficient evaporation process close to the entrance cone enables the routine use of high LC flow rates up to 2 mL min in ESI mode The newly formed ions then enter the flow focusing region through the entrance cone This is due to the following e The high electric field the insert capillary is at 3 to 5 kV with respect to the rest of the source which is typically at 20 to 30 V e The gas flow into the flow focusing region Ions then exit the flow focusing region and pass into the RF lens The RF lens hexapole hel
40. have been established for ThermoQuest manuals for the following e Datainput e Notes Cautions and WARNINGS Topic headings Data Input Throughout this manual the following conventions indicate data input and output via the computer e Prompts and messages displayed on the screen are represented in this manual by capitalizing the initial letter of each word and italicizing each word e Input that is to be entered by keyboard or buttons that are to be clicked on by the mouse is represented in bold face letters Titles of topics chapters and manuals also appear in bold face letters e For brevity expressions such as choose File Directories are used rather than pull down the File menu and choose Directories e Any command enclosed in angle brackets lt gt represents a single keystroke For example press lt F1 gt means press the key labeled F7 e Any command that requires pressing two or more keys simultaneously is shown with a hyphen connecting the keys For example press lt Shift gt lt F1 gt means depress and hold the Shift key and then press the F1 key Finnigan AQA Hardware Manual Xi Manuals Page Search Manuals Feedback Web _ Read This First Typographical Conventions FINNIGAN AQA xii Notes Cautions and Warnings Notes Cautions and WARNINGS are displayed in boxes such as the one below Note Boxes such as this are used to display Notes Cautio
41. it should also be replaced Clean rotary pump oil is a clear straw color Finnigan AQA Hardware Manual 5 21 Manuals Page Search Manuals Feedback Web Routine and Preventive Maintenance The Rotary Pump FINNIGAN ACXA Adding Oil WARNING Vent the instrument before adding oil Attempting to add oil while the pump is running could result in serious personal injury from hot rotary pump oil The oil used in the Edwards E2M28 Rotary Pump is type Ultragrade 19 P N FM101067 1 Turn Operate Off and vent the instrument Refer to the chapter Shutting Down and Restarting the System for information on turning Operate Off and venting 2 Remove the oil filler plug marked Oil from the top of the pump Pour the oil into the pump until the oil level in the viewing window is close to but not above the upper mark 5 22 Finnigan AQA Hardware Manual Thermo 2uest Routine and Preventive Maintenance FINNIGAN AQA The Borary Pump Changing the Rotary Pump Oil The fluid in the rotary pump should be replaced at least once every six months When replacing the oil also replace the foreline trap pellets The oil used in the Edwards E2M28 Rotary Pump is Ultragrade 19 P N FM101067 WARNING Wear gloves when changing the oil Avoid contact with the pump oil it may contain dissolved residues from analyzed samples Observe appropriate disposal requirements when discarding the used oil 1 Turn O
42. s A source flange o ring s is missing or damaged Replace the o ring s The entrance cone is damaged Replace the entrance cone The exit cone is damaged or missing Replace the exit cone There is excessive noise from the turbomolecular pumps Potentially faulty turbomolecular pump Call your local ThermoQuest Service Representative The turbomolecular pumps are tripping Potentially faulty turbomolecular pump Call your local ThermoQuest Service Representative MS Resolution Problems able 6 9 details for each MS resolution problem the symptom probable cause and remedy Table 6 9 Troubleshooting MS resolution problems Symptom Probable cause Remedy Unresolved peaks with LM HM Res 12 5 and ion energy 1 0 Faulty electronics Please call your local ThermoQuest Service Representative Poor resolution and low sensitivity To get ions you must increase the ion energy to 2 1 5 Dirty prefilters or quadrupole Please call your local ThermoQuest Service Representative The sensitivity fine but there is no resolution Failed DC voltage Run the instrument diagnostics If the diagnostic test fails call your local ThermoQuest Service Representative Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA ThermoC2uest Troubleshooting R
43. seal and so on Thermo 2uest Finnigan AQA Hardware Manual 6 27 TE Page Search Manuals Feedback web Troubleshooting HPLC System Troubleshooting FINNIGAN AG 6 28 Finnigan AQA Hardware Manual Thermo 2uest Chapter 7 Shutting Down and Restarting the System Contents 1 Introduction 2 Instrument Standby and Shutdown n Between Analytical Runs eese eee nren nennen nenne ANETDRUCICMEEREEEEEEEEERREEEEEEEEEEESEEREEES Two Weeks or More 3 Restarting the System re switch on Checklist System Start up Procedure umping Down the Finnigan AQA ThermoC2uest Finnigan AQA Hardware Manual T i TTE Page Search Manuals Feedback web Shutting Down and Restarting the System Conten FINNIGAN ACXA 7 ii Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA Shutting Down and Restarting the System Introduction ThermoC2uest 7 1 Introduction This chapter provides details of how to shut down the Finnigan AQA system for a short period up to 2 weeks or for a longer period It also describes how to restart your system following a long term shutdown Finnigan AQA Hardware Manual 7 1 Manuals Page Search Manuals Feedback Web _ Shutting Down and Restarting the System Instrument Standby and Shutdown FINNIGAN AG 7 2 Instrument Standby and Shutdown
44. source voltages For example the Finnigan AQA can be programmed to acquire data at source voltages of 20 40 and 60 V on an alternating scan basis within a single acquisition The benefits of setting up acquisitions in this way are e The optimum source voltage for a particular ion can be determined in one acquisition for compounds where sample volume is at a premium e The intensity of fragment ions can be maximized to gain structural information Fragmentation at increased source voltages is useful for most compounds For example using source fragmentation of salbutamol in electrospray ionization a number of confirmatory fragment ions can be generated and their intensity maximized see The mechanism for the formation of the fragment ions is characteristic for not only salbutamol but also for related B agonists such as clenbuterol terbutaline and metaproterenol It involves loss of water 18 amu resulting in the fragment ion at m z 222 middle trace and an additional loss of the tert butyl group 56 amu resulting in the fragment at m z 166 lower trace Note The Finnigan AQA uses the term AQAmax to represent source voltage Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web FINNIGAN AQA Introducing the Finnigan AQA The Source an Introduction to API Techniques ThermoC2uest 240 Protonated molecule at m z 240 Source voltage 10V OH HO 24
45. the Probe Remove the probe cover plate Refer to the topic Removing the RF Hexapole in the chapter Routine and Preventative Maintenance for details of this procedure 2 Ensure that the ESI insert and ESI ceramic gas nozzle are fitted These parts are used in the alignment procedure Refer to the topic Setup for ESI in the chapter Changing Ionization Modes for details 3 Loosen the two screws that secure the probe mounting block in position 4 Align the probe on two axes see Figure 6 4 so that e The axis of the ESI insert is in line with the entrance cone orifice e The end of the ESI ceramic gas nozzle is in line with the edge of the entrance cone screws securing the probe mounting block in positiion entrance cone elem O ESI ceramic gas nozzle ESI insert Figure 6 4 Aligning the probe 6 10 Finnigan AQA Hardware Manual ThermoC2uest FINNIGAN AQA Troubleshooting Troubleshooting Tables Inlet System Chromatography Problems able 6 3 details for each inlet system chromatography problem the HPLC System Troubleshooting symptom probable cause and remedy See on page 6 22 for further information Table 6 3 Troubleshooting inlet system chromatography problems Symptom Probable cause Remedy Low sensitivity Unstable solvent flow Incorrect solvents Poor sample preparation Refer to the topic Low Sensitivity Problems on page 6
46. to switch on Communications failure See Problems on page Line extender cable Reconnect disconnected Thermo 2uest Finnigan AQA Hardware Manual 6 3 Troubleshooting Troubleshooting Tables FINNIGAN AQA Symptom Probable cause Remedy Pumps switch on but fail to generate vacuum Source block not inserted correctly Remove source block and refit See the topic The Source Block in the chapter Routine and Preventative Maintenance for details Air is leaking into the system Check all source o rings and seals Rotary pump foreline trap pellets need replacing Refer to the chapter Routine and Preventative Maintenance for details up or replacing Rotary pump oil needs topping Refer to the chapter Routine and Preventative Maintenance for details Rotary pump gas ballast open Close gas ballast Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN ACXA Troubleshooting Troubleshooting Tables Low Sensitivity Problems Sensitivity is determined by the ratio of signal to noise Before attempting a diagnosis determine whether the problem is due to a weak signal or excessive noise by reference to a previous known good spectrum details for each low sensitivity problem the symptom probable cause and remedy Table 6 2 Troubleshooting low sensitivity proble
47. to the open position see Figure 2 6 Unscrew and remove the PEEK finger tight fitting from the PEEK union at the inside edge of the source enclosure Remove the ESI insert P N 9227 66 and its connecting blue stripe PEEK tubing Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web Changing lonization Modes FINNIGAN AQA Removal of ESI Caution Exercise care when handling the ESI insert because it is fragile and may be damaged easily re ESI insert thumb nut insert retaining latch Figure 2 6 Removing the ESI insert Thermo 2uest Finnigan AQA Hardware Manual 2 7 Manuals Page Search Manuals Feedback Web Changing lonization Modes Setup for APCI FINNIGAN AQa 2 5 Setup for APCI The starting point for this procedure is a probe with no insert installed WARNING Allow the source block and probe heater assembly to cool before changing ionization modes 1 Fit the APCI insert P N 9227 65 into the probe Caution Exercise care when handling the APCI insert because it is fragile and may be damaged easily orange stripe PEEK tubing x N EE Figure 2 7 APCI insert 2 Secure the orange stripe PEEK tubing of the APCI insert to the PEEK union at the inside edge of the source enclosure using the PEEK finger tight fitting 2 8 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedba
48. two turbomolecular pumps All the pumps are controlled by the data system Finnigan AQA Hardware Manual ThermoC2uest TTE Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Introducing the Finnigan AQA The Data System 1 8 The Data System The data system has complete control of the Finnigan AQA system and runs on a Microsoft Windows NT platform Software Xcalibur M software controls the Finnigan AQA MS detector When Xcalibur is run the Home Page is displayed see Figure 1 22 In addition Xcalibur also runs the Finnigan AQA Server see Figure 1 23 The Home Page The Home Page opens to show a road map view of the data system b Road Map Home Page Ei x File Actions View Tools GoTo Help Browser Browser Browser For Help press F1 NUM 9 10 98 3 21PM 4 Figure 1 22 The Xcalibur Home Page Road Map view Finnigan AQA Hardware Manual 1 31 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Data System 1 32 FINNIGAN AQA The icons shown on the road map provide an easy way to access all the major modules of the data system These modules are e Instrument Setup Use Instrument Setup to configure the Finnigan AQA and all your LC equipment for acquisition This information is saved as an instrument method e Processing Setup Use Processing Setup to specify all parameters for processing reporting and m
49. various injection loop volumes although they are most suitable for volumes up to 100 uL The injection valve rotor face is easily damaged by solid particles entering the injector and subsequent loading and injecting The most common source of damage is from stainless steel tube filings The rotor is easily replaced refer to the manufacturer s manual Injectors are prone to blockage if dirty samples are injected or particles from the mobile phase or a worn pump seal block the passages Strip and clean the injector regularly Most manual injection valves require a square tipped needle Avoid pointed or tapered needles because they can become stuck in the injector or scratch the rotor seal Some autosamplers use a side port needle to prevent septum coring UV Detectors UV detectors are the most widely used LC detectors and are often used in line with LC MS instruments The three common types of UV detector are single wavelength one channel multi wavelength four channels with two outputs combinations are possible and diode array a scanning UV detector Finnigan AQA Hardware Manual 6 25 Manuais Page Search Manuals Feedback Web Troubleshooting HPLC System Troubleshooting FINNIGAN AG UV Detector Problems Temperature wavelength selection and the detector time constant affect noise and drift If the environmental temperature varies greatly baseline drift can occur Wavelength selection can influenc
50. 1 EM T 50 75 100 125 150 175 200 225 250 275 300 240 Fragment ion at m z 222 100 Source voltage 25V M H H20 NH IB HO Sul 2 uU 96 222 HO 241 50 75 100 125 150 175 200 225 250 275 300 7 m n Fragment ion at m z 166 Source voltage 35V M H H20 tBu NH HO 148 Na 166 HO 241 MUR MER PRIN iiu PPE idi eu ueu o mf 50 75 100 125 150 175 200 225 250 275 300 Figure 1 14 Source fragmentation of salbutamol in electrospray ionization Optimum Response for Confirmatory lons When acquiring fragment ions for confirmation purposes the applied source voltage per compound would require some optimization to maximize the intensity of these ions It is generally observed that small changes to the source voltage result in only small intensity changes and thus fine tuning of this voltage is usually not critical typically 5 V is adequate Finnigan AQA Hardware Manual 1 19 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AQ Source Voltage Ramping Source voltage ramping can be used in Full Scan operation see page 1 35 in electrospray when the compound of interest forms multiply charged ions A spectrum similar to that in Figure 1 15 will be produced showing the multiply charged envelope m z 700 800 900 1000
51. 1 2 2 Remoyalof APCL e ertet ttr netter intere eriee rte Sev ede guesses Eae ree UEM eden 2 2 CHE ao dic RR REOR ERROR RE RR PLE S 2 3 2 4 Removal Of A E ceri ER ERE RA REY EC E UAR Y REC RI R ERR AN ORE RR REGE A rage EE ea 2 6 P 3 uSBDUDTOE NP Te susiep eis eeacyt dense o initum E eset Ente due T ANNA AE RT 2 8 LC MS and AQA HOW qu escenseskcedcteskcsquekscceuMdebcku e eI iae conu e HR HAR HH CHA QUeHE E HUM CORR CON HER EXHN E PM cud UY 3 i 3r Tittoduclonmznc neges aped NIIS IS UIN IIS 3 1 3 2 LC MS Considerations reete etie eei eee EE e RE ee ERR Re atr ER ERR OUR Ree dci Prades 3 2 BIOW RAtES 3 2 HPLC Solvents and Mobile Phase Additives sese 3 3 3 3 Setting up AQA POW e 3 7 3 4 Flow Splitting cc eccccecccssscsseeseeecseeeseeeeceseeseeseceaecaseeeesseceaeesesseeeaesaesessaecsseeeesaecaeeseseeseaeens 3 12 AQA Sample Infusion SySbelli ceace acerca sean i deep xii HER HEY CENE dV Ce NI OUR Q EX SR ERN CIV RC U UE Ei ERR CUN 4 i 4 1 Jdntroduction iere sterii tertie ia ee ce Ee ert e et essen es rige EE 4 1 i aui Rc 4 2 4 3 Setting up the AQA Sample Infusion System sese 4 3 Routine and Preventive Maintenance 55 csccscccvssesscesscctsecesosstcoassctacensseciccosessucsadoonseciscasccasisssseess 5 i OMMER C oLa E e E COI ECT E 5 1 5 2 Maintenance Schedule nae Henn eibeteiihitditinte is ibn RRS
52. 2 handling insert 2 2 2 7 2 8 heater wires and thermocouple 5 16 phosphoric acid 3 5 removing the source block 5 9 tetrahydrofuran THF 3 5 centroid 1 35 changing ionization modes description 2 i hot parts Warning 2 2 2 3 2 6 2 8 checklist pre switch on 7 4 chemical ionization 1 15 chromatogram types of 1 33 chromatography chromatographic considerations 3 2 problems 6 11 cleaning entrance cone 5 6 ESI ceramic gas nozzle 5 3 ESI insert 5 3 flushing inserts 5 3 hexapole RF lens 5 14 rear panel fan filters 5 25 source block 5 7 communication problems 6 16 problems table 6 16 comparison of ESI and APCI table 1 24 consumables 8 2 contamination in HPLC systems 6 23 corona pin ionization mechanism 1 15 position figure 2 10 D Dalton Da 1 4 data See raw data data system 1 31 detector 1 29 detergents 3 4 Finnigan AQA Hardware Manual 1 Manuais Page Search Manuals Feedback Web _ FINNIGAN AQA Index diagnostics flow focused source 1 3 running 6 20 foreline trap dialog box pumping connections figure 5 24 Finnigan AQA Properties figure 1 33 Instrument Diagnostics and Optimizations figure 6 20 dimethyl sulphoxide 3 4 E electrospray See ESI entrance cone cleaning 5 6 storage and handling Caution 5 12 ESI applications 1 23 comparison with APCI table 1 24 introduction 1 10 ion generation 1 11 removal 2 6 setup 2 3 source figure
53. 2uest Head This First Abbreviations Abbreviations The following abbreviations are used in this and other Finnigan AQA manuals and in the online Help A ac ADC amu AP APCI API ASCII b B baud rate C cfm CD CD ROM CI CIF CIP cm cm CPU CRM Ctrl d Da DAC dc DDS DS DSP EI ampere alternating current analog to digital converter atomic mass unit acquisition processor atmospheric pressure chemical ionization atmospheric pressure ionization American Standard Code for Information Interchange bit byte 8 b data transmission speed in events per second degrees Celsius cubic feet per minute compact disc compact disc read only memory chemical ionization Carriage Insurance Freight Carriage and Insurance Paid To centimeter cubic centimeter central processing unit of a computer consecutive reaction monitoring control key on the terminal keyboard depth dalton digital to analog converter direct current direct digital synthesizer data system digital signal processor electron ionization Finnigan AQA Hardware Manual vii Manuais Page Search Manuals Feedback Web _ Head This First Abbreviations FINNIGAN AQA viii lt Enter gt EMC ESD ESI eV f F FID FOB FPD ft FTP GC GC MS GND GPIB GUI HPLC HV Hz ICIS ICL IEC IEEE in VO k kg lt Enter gt key on the terminal keyboard electromagnetic compatibilit
54. AQA Thermo 2uest Shutting Down and Restarting the System Instrument Standby and Shutdown Two Weeks or More If the Finnigan AQA system is unlikely to be used for an extended period longer than 2 weeks perform a full shutdown 1 Open the Finnigan AQA Tune window see page 7 2 2 Choose Instrument Gas or click on the Toggle Gas toolbar button to switch the nitrogen gas flow Off 3 Choose Instrument Operate or click on the Toggle Operate toolbar button to switch Operate Off 4 Right click on the Finnigan AQA Server in the Windows Taskbar and choose Vacuum Vent to vent the system The Server is displayed as an icon in the Windows Taskbar just to the left of the time display see Figure 7 1 43 Stat X Road Map Home Page BR zsm Figure 7 1 The taskbar showing the Server icon The Server is shown as three lights e The green top light represents the Vacuum status e The red middle light represents the Operate status e The yellow bottom light represents the API Gas status All the lights are automatically switched off as the instrument is shut down Refer to the topic The Server in the chapter Introducing the Finnigan AQA for more information on the Server 5 Exit from Xcalibur and shut down the PC in the usual way Ensure that you have switched off the PC monitor printer and any other associated hardware Switch off the instrument and unplug it from the mains Carry out any column con
55. AQA Hardware Manual 2 i TTE Page Search Manuals Feedback web Changing lonization Modes Contents FINNIGAN AQa 2 ii Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Changing lonization Modes Introduction 2 1 Introduction Use the information in this chapter in conjunction with the ESI and APCI setup animations on the Finnigan AQA CD shipped with your system The chapter is divided into the following sections e Removal of APCI e Setup for ESI e Removal of ESI e Setup for APCI To change from APCI to ESI follow removal of APCI and then setup for ESI Similarly to change from ESI to APCI follow removal of ESI and then setup for APCI Finnigan AQA Hardware Manual 2 1 TTA Page Search Manuals Feedback web Changing lonization Modes Removal of APCI FINNIGAN AQa 2 2 Removal of APCI The starting point for this procedure is the source setup for APCI operation with the LC and gas flows off and the probe cooled WARNING Allow the source block and probe heater assembly to cool before changing ionization modes 1 Loosen the thumb nut and drop the retaining latch to the open position see Figure 2 1 2 Unscrew and remove the PEEK finger tight fitting from the PEEK union at the inside edge of the source enclosure 3 Remove the APCI insert P N 9227 65 and its connecting orange st
56. AQA Hardware Manual ThermoC2uest TA Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest AQA Sample Infusion System Setting up the AQA Sample Infusion System 4 3 Setting up the AQA Sample Infusion System Use the following information in conjunction with the setup and maintenance animations on the Finnigan AQA CD shipped with the instrument These instructions show how to configure the AQA sample infusion system to introduce tuning and mass calibration samples into the source They assume that the source is setup for electrospray ionization If your source is not setup for ESI refer to the chapter Changing Ionization Modes 1 Unscrew the AQA reservoir from its support and empty out any remaining liquid 2 Place an Eppendorf sample vial P N FM100785 containing your sample into the tripod sample vial holder P N FM100764 with the lid open Empty AQA Eppendorf vial tripod reservoir containing the sample Figure 4 2 Placing sample vial and tripod into the empty AQA reservoir Place the tripod sample vial holder into the empty AQA reservoir 4 Check the integrity of the o ring seal Replace the o ring P N FM 100200 if it is damaged 5 Screw the reservoir back into its support Finnigan AQA Hardware Manual 4 3 Manuals Page Search Manuals Feedback web AQA Sample Infusion System Setting up the AQA Sample Infusion System FINNIGAN AG 6 Loosen the Swagelok nut on the
57. FUNCTION Check one only Q Other Q Administration Q Lab Management Q Operator Q Other Name Title Compan ne Thank You Address ZZ City State Postal Code T i ee Country Telephone Ext Thermo 2u est Finnigan AQA Serial Date purchased Please fold this sheet closed stamp it and drop it in the mail Manuals Page Search Manuals Feedback Web Technical Publications Manager ThermoQuest Crewe Road Wythenshawe Manchester M23 9BE UK MassLab Ltd 72 Crewe Road Wythenshawe I J Manchester M23 9BE Sm UK Tel 44 161 946 1060 Thermo 2uest Fa 161 998 9882 EU DECLARATION OF CONFORMITY The EU Directives covered by this Declaration 89 336 EEC Electromagnetic Compatibility Directive amended by 92 31 EEC amp 93 68 EEC 73 23 EEC Low Voltage Equipment Directive amended by 93 68 EEC 93 68 EEC CE Marking Directive The Products covered by this Declaration The Finnigan AQA formerly Navigator II mass spectrometer for LC MS The Basis on which Conformity is being Declared The products identified above comply with the EU directive 89 336 EEC by meeting the following standards EN55022 Class A 1994 Limits and methods of measurement of radio interference characteristics of information technology equipment EN50082 1 1992 Electromagnetic compatibility Generic immunity standard Part 1 Residential commercial and light industry FCC Part 15 SubPart B Class A Digital Devices FCC EMC
58. Manuals Feedback Web _ AQA Sample Infusion System Setting up the AQA Sample Infusion System FINNIGAN AG The graph in Figure 4 6 shows the relationship between the pressure within the AQA reservoir and the sample infusion rate Sample infusion rate uL min 0 5 10 15 20 25 Resevoir pressure psig Figure 4 6 Graph of sample infusion rate against reservoir pressure fused silica dimensions length 650 mm ID 0 1 mm OD 0 36 mm 4 6 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web AQA Sample Infusion System FINNIGAN AQ Setting up the AQA Sample Infusion System 10 Check that liquid is emerging from the end of the ESI insert The flow rate should be approximately 10 uL min liquid drop emerging from the ESI insert Figure 4 7 Liquid emerging from the end of the ESI insert 11 Stop sample infusion by depressurizing the AQA reservoir Pull out the mini regulator adjuster and turn anti clockwise Stopping the flow allows time for the probe heater to warm up and stabilize at the required temperature for sample infusion 12 Close the source Follow step 9 to pressurize the AQA reservoir Introduce the sample into the source when the gas flows have been activated and the probe has reached the required temperature Note Allow time for the probe heater to warm up and stabilize at the required temperature before commencing sample infusion Therm
59. N iu FORT 6 1 6 2 Troubleshooting Tables auossukased doses Qui puis t iiie ramus heeded brigade le Eee 6 2 General arant E EEE EAEE 6 3 Low Sensitivity Problems eerie ia a a aeta nitate ke enda 6 5 Inlet System Chromatography Problems eene 6 11 Sp ctral ur Sun MEI EPIM t iS 6 13 Calibration Problems eot e transeat Pe Lone al Deere Feed tUa eoe dan 6 14 ibtinnpadaci snsg eT 6 15 Communication Problems eese ener nre en rennen 6 16 Vacutim Problermis ite iter tO Hebe e E R ru tate Desire i Dec eds 6 17 MS Resolution Problems 1 nibii Leer Eoo Ee reae ee lat b a Ee Dee o ea Du p buceo 6 18 6 3 Resolving Common Prolene osi em x bee un OR SUE EH FH ROSA Ert LO SEDE CH HA Coe Y NUN et dU 6 19 Checking Finnigan AQA Power Supply Requirements eee 6 19 Rebootmg the PC etit Het te eneee poa e ep eso t de pe sel bene evet auge ice A roe 6 19 Running Finnigan AQA Tuning Diagnostics 6 20 6 4 HPLC System IeolblosoODBE oci eoi datu erepbss visite pu x bi Un eco p p a MEME e SEES CE 6 22 Buffers and Additives c scceecssssescesececeeecesecseeeeeesecsaecaceeeceaecseeeceeeecsaeeaceeeeeaeeaeeeeeaeeuee 6 22 Mobile Phase ReSeryOLt 5 cederet tpe rri Lee eite rs rte queer TEER E AEE gn 6 22 Bubble Problems and Degassing eene nennen eene rennen 6 22 Contamination in the LC System ooo
60. Number of each Part category part contained in the kit entrance cone o ring BS012 viton FM100231 disrupter pin o ring BS003 viton 5711003 vacuum line elbow o ring BS013 viton 5711013 source flange hexapole side o ring BS235 viton source flange source block side o ring 5711121 consumable BS121 viton AQA reservoir o ring BS131 viton FM100200 consumable Thermo 2uest Finnigan AQA Hardware Manual 8 3 Consumables and Spares Consumables FINNIGAN AQ Source Screws and Fixings Kit FM101066 Part description Part number Number of each Part category part contained in the kit source block screw FM100382 4 consumable M4 x 37LG c sunk head st stl probe cover plate screw FM100493 4 consumable M3 x 30LG c sunk head st stl probe washer 1150605 4 consumable M3 flat washer probe cover plate differential aperture 5311016 4 consumable plate screw M3 x 6LG c sunk head st stl entrance cone screw 5311023 10 consumable M3 x 8LG c sunk head st stl PEEK ZDV union securing screw 5313041 2 consumable M3 x 6LG cap head st stl source flange screw 5313047 4 consumable M5 x 12 cap head zinc plated exit cone screw 5314015 10 consumable M3 x 4LG ch head st stl probe screw 5314016 4 consumable M3 x 6LG ch head st stl hexapole stud nut 5321004 consumable MS st stl nut 8 4 Finnigan AQA Hardware Manual ThermoC2uest Consumables and Spares
61. URCE pumping To the BACKING pumping _ Foreline trap Pumping inlet i Lj Rotary pump v Figure 5 20 The rotary pump showing the foreline trap and the pumping connections to the rear of the Finnigan AQA Use Foreline Trap alumina pellets P N 6060116 For any additional information refer to the Foreline Trap manual provided l 2 5 24 Turn Operate Off and vent the instrument Remove the end cap from the foreline trap to gain access to the inner basket of alumina pellets Remove the basket from the foreline trap and empty its contents Refill with a new tin of pellets Reassemble the foreline trap Pump down the instrument to prepare for operation Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA Thermo 2uest Routine and Preventive Maintenance The Rear Panel Fan Filters 5 8 The Rear Panel Fan Filters The Finnigan AQA has two rear panel fans to cool the instrument internally Covering these fans are two fan filters that prevent dust and other particulate matter from entering the instrument It is necessary to periodically clean the filters as they can become blocked causing the Finnigan AQA to overheat position of fans on rear panel ANALOGUE OUT com Lore
62. alyzer and Detector 1 6 The Mass Analyzer and Detector The mass analysis and detection system comprises two main components e A quadrupole mass analyzer e A detector whose main component is a photomultiplier tube The hexapole RF lens helps to focus the ions before they are filtered according to their mass to charge ratio in the mass analyzer The analyzer in the Finnigan AQA is a quadrupole This is one of the most widely used types of analyzer and can be easily interfaced to various inlet systems By applying carefully controlled voltages to the four rods in the quadrupole only ions of a specific mass to charge ratio are allowed to pass through at any one time The ions then reach the detector whose main component is a photomultiplier tube The ions exit the analyzer and strike a conversion dynode which results in the emission of electrons The electrons are accelerated towards a phosphor screen producing photons The photons then strike the photocathode in front of the photomultiplier which then creates an electron cascade This cascade allows the tiny electron current to be magnified to about 1 000 000 times the original signal The current is then converted and amplified into a voltage signal that is analyzed and processed by the Finnigan AQA s on board data acquisition system The resultant peak information is sent to the data system Detector lon successfully transmitted by the mass analyzer gt Quadrup
63. ance Schedule FINNIGAN AQA 5 2 Maintenance Schedule able 5 1 is a list of routine maintenance procedures that should be carried out on the Finnigan AQA at the intervals specified The maintenance schedule provides only a rough guide to the frequency of maintenance tasks The appropriate frequency depends on instrument usage and the level of system induced contamination from samples and matrices Table 5 1 Maintenance schedule Freauency mmm Clean the source if a drop in sensitivity is seen during analysis or if there is a drop in sensitivity when performing the sensitivity verification test refer to the chapter Preparing for Daily Operation in the Finnigan AQA Getting Started manual see page Bl Clean and flush the inserts see page Check the oil level and color in the rotary pump and add oil if necessary see page Monthly 3 6 Monthly 6 Monthly Check the rear panel fan filters for blockage and clean if necessary see page Refer to the PC user guide supplied for cleaning the PC fan filters 5 2 Finnigan AQA Hardware Manual Thermo 2uest TA Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Routine and Preventive Maintenance The Electrospray and APCI Inserts 5 3 The Electrospray and APCI Inserts To extend their lifetime regularly flush both the inserts with solvent especially after prolonged use with buffers The ESI insert can also be st
64. anipulation of acquired data This information is saved as a processing method e Sequence Setup Use Sequence Setup to enter the details of the samples to be examined including instrument and processing methods and to control the acquisition of data e Qual Browser Use Qual Browser to examine acquired data both chromatograms and spectra in order to obtain more information about the compounds in the sample e Quan Browser Use Quan Browser to examine acquired data in order to obtain an accurate determination of the amounts of individual components present in a sample e Library Browser Use Library Browser to create your own libraries of spectra and to perform searches of those libraries The Server The Server is displayed as an icon in the Windows Taskbar It is shown in igure 1 23 just to the left of the time display si X Road iae Hore Page E 25m Figure 1 23 The taskbar showing the Xcalibur Home Page and Server The Server is shown as three lights e The green top light represents the Vacuum status e The red middle light represents the Operate status e The yellow bottom light represents the API Gas status Finnigan AQA Hardware Manual ThermoC2uest TTE Page Search Manuals Feedback web Introducing the Finnigan AQA FINNIGAN ACXA The Data System When all the lights are on the Finnigan AQA is in vacuum with Operate On and the API gas flowing In addition when the Finnigan AQA is pump
65. aseline is constant a bubble is likely but if the noise persists a failed lamp or external electrical problem is more likely Testing UV Detectors Test a UV detector by monitoring the output either via the analog inputs check output voltage or by viewing the UV detector display Injecting a solution of erythromycin for example should give a good response at a wavelength setting of 280 nm 6 26 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web Troubleshooting FINNIGAN AQa HPLC System Troubleshooting Preventative Maintenance and Spares Important practices to prevent LC system problems are e Filtering If possible filter solvents especially if buffers are being used and samples to prevent unwanted particulate matter from entering the pump and subsequently the Finnigan AQA e Degassing Thoroughly degas all solvents to prevent air from entering the pump to minimize problems associated with bubbles and to improve check valve operation e Flushing Regular flushing of the system to remove unwanted contaminants and to prevent build up of buffer residues will extend pump component lifetimes e Replacing pump seals The pump seals should be replaced regularly every 3 months with constant use Keep a stock of PEEK tubing and fittings frits filters and syringes It is helpful to have use of a manual injector valve with 10 uL loop and spares nuts ferrules rotor
66. ating to mass spectral data Calibration Problems relating to calibration Tuning Problems relating to tuning Communication Problems relating to communications between the various parts of the system and with Xcalibur Vacuum Problems relating to the vacuum system MS resolution Problems relating to MS resolution The tables describe the visible symptoms the probable cause of the problem and suggestions on how to remedy it Finnigan AQA Hardware Manual Thermo 2uest Troubleshooting FINNIGAN AQ Troubleshooting Tables General Problems able 6 1 details for each general problem the symptom probable cause and remedy Table 6 1 Troubleshooting general problems Symptom Probable cause Remedy System fails to power up System not plugged in or not switched on at the mains Plug in and switch on Mains supply problems Check mains supply conforms to the requirements of the Finnigan AQA system see Checking Finnigan AQA Power Supply Requirements on page 6 19 for details Rear panel fan fails to operate Fan filter is blocked and needs cleaning Clean the real panel fan filters Refer to the chapter Routine and Preventative Maintenance for details Fan is broken Contact your ThermoQuest service representative Rotary pump fails to switch on Pump not plugged in or not switched on Plug in Switch on Check circuit breaker Turbomolecular pump fails
67. bench top MS detector systems LC MS works with typical solvent compositions whether the separation is achieved by isocratic or by gradient elution Historically LC MS has been compatible only with volatile buffer systems using modifiers such as trifluoroacetic acid formic acid and acetic acid Phosphate buffers although extensively used in LC separations were not suited to LC MS due to rapid blocking of the ion sampling region caused by the deposition of involatile phosphate salts The self cleaning AQA API source allows for extended periods of operation in LC MS with chromatographic buffers such as phosphates or ion pairing agents and samples in dirty matrices API using Electrospray ESI or Atmospheric Pressure Chemical Ionization APCD interfaces has proved to be invaluable in meeting sensitivity requirements in quantitative methods It can also provide structural information which is complementary to techniques such as NMR and infra red spectroscopy This introduction focuses on the principal components of the system Thermo 2uest Finnigan AQA Hardware Manual 1 1 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA System Overview 1 2 System Overview FINNIGAN AQA The Finnigan AQA MS detector is an integral part of the LC detection system Key points of the system are The sample is introduced into the ion source using an LC system possibly through a column In an API MS dete
68. ce Under operating conditions however both the sample ions and the charged liquid droplets containing any involatile components if they are present are deflected by the electric field towards the entrance orifice This leads to a gradual build up of involatiles and a concomitant loss in sensitivity with time The self cleaning AQA source delivers a constant low flow of solvent the AQA flow to the edge of the inlet orifice helping to prevent a build up of involatiles during an LC MS run The sample ions enter the flow focusing region of the source through the entrance cone Flow focusing has been designed to eliminate the need for electrostatic lenses as a means of efficient extraction of ions into the mass analyzer The source chamber between the entrance and exit cones is designed such that the gas flow is disrupted after passing through the entrance orifice see Figure 1 7 This has the effect of increasing the number of ions in the region adjacent to the exit cone orifice which in turn increases the ion transmission efficiency through the exit cone and into the mass analyzer The entire flow focusing region is held at the same electric potential forming a field free region Finnigan AQA Hardware Manual 1 9 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AG To the mass analyzer Exit cone o o Rotary pump Flow d
69. ce representative or LC system manufacturer The instrument stops and displays the message waiting for contact closure The contact closure cable is incorrectly fitted Check that the cable is attached correctly Replace it if appropriate Xcalibur crashes at the start of data acquisition The Xcalibur software or raw file has become corrupted Delete the raw file Reboot the PC and reload the software if necessary 6 16 Finnigan AQA Hardware Manual Thermo 2uest Manuais Page Search Manuals Feedback Web Troubleshooting FINNIGAN aQu Troubleshooting Tables Symptom Probable cause Remedy The system crashes High voltage breakdown from Clean the ESI ceramic jet insulator Refer at times other than the ESI ceramic jet insulator to the topic Cleaning the ESI Insert and the start of data Ceramic Gas Nozzle in the chapter acquisition Routine and Preventative Maintenance Replace the ESI ceramic jet insulator if it is damaged High voltage breakdown from Increase the probe temperature and or excessive condensation in the reduce the flow rate into the source source enclosure enclosure High voltage tracking due to Clean the source Refer to the topic The dirty source Source Block in the chapter Routine and Preventative Maintenance Vacuum Problems able 6 8 details for each vacuum problem the symptom probable cause y and remedy Table 6 8 T
70. chedule description 5 2 table 5 2 mass analyzer 1 29 mass detection 1 4 mass range chromatogram 1 33 Thermo 2uest mass spectrum introduction 1 33 spectral problems 6 13 spectral problems table 6 13 mass to charge ratio 1 4 MCA 1 37 methanol 3 3 mobile phase additives 3 3 modes of acquisition 1 34 molecule deprotonated 1 13 protonated 1 13 multi channel analysis 1 37 multiply charged ions 1 14 N nebulizing gas 1 12 1 15 non volatile salts 3 4 normal phase solvents 3 4 Notes AQA flow 1 26 AQA flow solvent 3 7 assembling hexapole RF lens 5 19 changing the rotary pump oil 5 23 cleaning rear panel fan filters 5 26 disassembling hexapole RF lens 5 17 field free source region 1 12 1 16 Finnigan AQA under vacuum 7 2 flow splitting 3 13 flushing the inserts 5 3 removing hexapole RF lens 5 14 rotary pump maintenance 5 21 running tune diagnostics 6 21 sample infusion 1 27 sample infusion flow rate 4 2 sample infusion probe temperature 4 7 source voltage ramping 1 21 starting vacuum pumps 7 5 troubleshooting calibration problems 6 15 troubleshooting tuning problems 6 15 O oil adding oil 5 22 changing rotary pump oil 5 23 checking oil level 5 21 checking the color 5 21 orthogonal probe 1 3 P part categories 8 1 parts kit consumables 8 2 source o rings 8 3 source screws and fixings 8 4 parts lists 8 i Finnigan AQA Hardware Manual 3 Index
71. ck web Changing lonization Modes FINNIGAN AQA Setup for APCI LC tubing APCI insert insert insulated plug retaining latch Figure 2 8 Installing the APCI insert and securing with the retaining latch 3 To hold the insert in place secure the retaining latch using the thumb nut use finger tight pressure Secure corona pin in Corona pin lowered position using the nut into the APCI position Figure 2 9 Lowering the corona pin Thermo 2uest Finnigan AQA Hardware Manual 2 9 Manuais Page Search Manuals Feedback Web _ Changing lonization Modes Setup for APCI FINNIGAN AQA 4 Lower the corona pin into the APCI position and secure with the thumb nut see Figure 2 9 When looking at the probe and corona pin end on ensure that the pin is central and protrudes into the path of the probe by 1 mm equal distance corona pin e o m A probe Figure 2 10 The position of the corona pin relative to the probe for APCI 5 Insert the insulated plug P N FM100507 into the APCI position see Figure 2 8 for identification of the insulated plug 2 10 Finnigan AQA Hardware Manual Thermo 2uest Chapter 3 LC MS and AQA Flow Thermo 2uest Finnigan AQA Hardware Manual TTE Page Search Manuals Feedback web LC MS and AQA Flow Introduction FINNIGAN AQa 3 ii Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedbac
72. ctor the part of the source where ionization takes place is held at atmospheric pressure giving rise to the term Atmospheric Pressure Ionization API In ESI the sample is ionized in the liquid phase whilst in APCI ionization occurs in the gas phase In both cases efficient desolvation is needed to remove the solvents from the sample Ions now in the gas phase are passed through the mass analyzer and are collected at the detector The detected signal is sent to the data system and stored ready for processing LC System Sample introduction 4 LC Column Separation lon Source Mass Analyzer Detector lonization amp Sorting of ions gt Detection transmission of ions Vv Turbomolecular pata System amp rotary pumps windows NT Y Wk Molecular weight information Structural information Positive identification Quantitative information Figure 1 1 The key components of the Finnigan AQA API LC detection system 1 2 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Introducing the Finnigan AQA System Overview The main features of the Finnigan AQA MS detector are e Dual ESI APCI orthogonal probe e Self cleaning API LC MS interfac e e Flow focused source eliminating the need for electrostatic focusing Detec
73. ctrospray is to use the AQA sample infusion system Note Due to the low flow rates involved direct sample infusion is normally used only with electrospray In APCI a sample can be infused into the source using a splitter Infuse the sample into a suitable LC flow for example 0 5 mL min via the splitter before the sample enters the source Functional Description As shown in Figure 1 20 the sample infusion system consists of a pressurized reservoir containing an Eppendorf sample vial supported by a tripod vial holder and a fused silica capillary One end of the capillary is inserted into the Eppendorf sample vial contained within the reservoir while the other end is attached to the sample introduction probe When the pressure in the AQA reservoir is increased the sample is forced through the fused silica capillary and infused directly into the source The pressure in the reservoir can be controlled and hence the sample infusion flow rate Finnigan AQA Hardware Manual 1 27 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Sample Infusion System FINNIGAN AG to sample introduction probe Eppendorf sample vial fused silica capillary Figure 1 20 The components of the sample infusion system 1 28 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web Introducing the Finnigan AQA FINNIGAN AQ The Mass An
74. ded acquisition Profile data files tend to be significantly larger than centroided ones and the scan speeds used tend to be slower than when acquiring centroided data 100 303 504 a 283 325 300 325 350 3 Figure 1 27 Full scan profile spectrum of D raffinose radhen a 400 275 75 425 450 475 500 525 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA FINNIGAN ACXA The Data System MCA The third type of full scan acquisition is MCA Such data can be thought of as summed profile with only one intensity accumulated scan being written to disk for a given experiment see Figure 1 28 As each scan is acquired its intensity data is added to the accumulated summed data of previous scans An advantage of MCA is that although noise will accumulate at the same rate as sample related data noise is random and therefore its effects will be reduced over a number of scans This will emphasize the sample related data and improve signal to noise A further advantage of MCA is that data is written to disk only at the end of an experiment therefore significantly less storage space is required MCA cannot be used for time resolved data because an MCA raw file contains only one scan Therefore MCA is not used during a chromatographic run Generally it is used to acquire infusion or loop injected samples of fairly weak concentrat
75. ditioning that may be required and shut down the LC and associated hardware Follow the instructions in the documentation supplied by the manufacturer Close the nitrogen gas cylinder at the main regulator 9 Switch off the water chiller once the system has cooled only applies if this option is fitted to your system Finnigan AQA Hardware Manual 7 3 TTE Page Search Manuals Feedback web Shutting Down and Restarting the System Restarting the System FINNIGAN AQA 7 3 Restarting the System This section describes how to restart the system Following a long term shutdown e Carry out the visual checks which form the pre switch on checklist e Follow the system start up procedure e Pump down the Finnigan AQA Once you have completed these procedures the system is ready for tuning and calibration see the Finnigan AQA Getting Started manual for details Pre switch on Checklist Before you switch on the system after an extended shutdown period a major overhaul or instrument relocation perform a number of visual checks on the system These include e Connections check e Data system connections e LC and MS power cables e LC and MS communication cables e LC check e Any gas supplies to the LC and associated hardware e Quantity of HPLC mobile phase e MS check e Water cooling connections only applies if this option is fitted to your system e API gas supply Finnigan AQA Hardware Manual ThermoC2uest
76. e Maintenance The Hexapole RF Lens FINNIGAN AG 5 Remove the two screws P N 5314016 and washers P N 1150605 that secure the probe mounting block in position see Figure 5 15 Note that the top screw is under the hexagonal spacer in the figure Swing the probe forward and to the left out of the path of the source flange Caution Do not bend the heater wires and thermocouple as the probe is moved to one side because this will damage the wires and lead to heater failure heater wires and thermocouple screws securing the probe mounting block in positiion Figure 5 15 Bringing the probe out of the path of the hexapole 6 Remove the two source flange screws P N 5313047 Reinsert the source block screws P N FM100382 into the source flange Use these to remove the hexapole which is attached to the source flange 5 16 Finnigan AQA Hardware Manual ThermoC2uest TIE Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Routine and Preventive Maintenance The Hexapole RF Lens source Screws source flange screws Figure 5 16 Removing the hexapole 8 Slide the hexapole forward to remove it from the instrument Disassembling and Cleaning the RF Hexapole Unscrew the three nuts holding the hexapole in place on the source flange studs Note Behind the nuts and hexapole are springs Exercise care when unscrewing the nuts Finnigan AQA Hardware Manual 5 17
77. e background noise and signal to noise ratios In general lower wavelengths result in increased signal for the sample as well as the background noise Balance the gain in signal against the increase in noise when selecting lower wavelengths The detector time constant acts as an electronic filter to reduce baseline noise Set the time constant to 1 10th of the peak width 10 points per peak Solvent selection is influenced by the wavelength to be monitored for example methanol is good for gradient work at 254 nm but at 215 nm it creates unacceptable baseline drift Acetonitrile has much lower absorbance at low wavelengths and is suitable down to 200 nm Contaminated solvents can cause high background Deuterium lamps should last for 1000 hours Noise spikes in the detector can arise from lamp filament flicker Detector cells are prone to trapping air bubbles from the mobile phase or micro particulate matter from the column The windows can also become clouded by polymerized organic material with long term use Solve bubble problems in the cell by using a thoroughly degassed mobile phase assuring that the fittings are leak free and applying a slight backpressure with a detector back pressure device The cell should be flushed daily with the rest of the system Noise spikes can arise from lamp problems air bubbles or external electrical interference This can be determined by setting the flow at zero and observing the baseline If the b
78. e from incorrect selection of internal diameter poor cutting and fittings Typical internal diameters are 0 020 between the pump and autosampler and 0 010 or less between the autosampler and UV detector and or column Cut stainless steel tubing with an abrasive wheel cut off machine a rotary cutter for example Terry tool or a triangle needle file Flush the tubing with solvent to remove any filings before connecting to the LC system When using stainless steel fittings take care not to over tighten as the tubing can become crushed and the flow restricted The ferrules can also be distorted leading to leaks Different brands of ferrules look different but for the most part they are interchangeable when they are new The primary difference between different brands is the distance of the extension of the tube past the ferrule WARNING Do not use stainless steel tubing to connect directly to the source in electrospray mode This could result in an electric shock due to the high voltage present on the insert capillary PEEK Poly Ether Ether Ketone Tubing This is now a widely used alternative to stainless steel tubing in high pressure parts of the system It is compatible with most LC solvents except THF tetrahydrofuran and methylene chloride It works well to a reasonably high pressure is easy to cut and route and is less expensive than stainless steel PEEK comes in eight different internal diameters that are color cod
79. e paper taking care not to blunt the end of the pin Sonicate the pin in methanol ESI APCI selector jumper insulated plug incorrectly inserted Move the insulated plug to the correct position Refer to the chapter Changing lonization Modes Incorrect ESI ceramic gas nozzle position Adjust to correct setting Refer to the topic Setup for ESI in the chapter Changing lonization Modes Thermo 2uest Finnigan AQA Hardware Manual 6 7 Manuals Page Search Manuals Feedback Web Troubleshooting Troubleshooting Tables FINNIGAN AQA Symptom Probable cause Remedy Weak signal continued Dirty ESI ceramic gas nozzle Clean or replace the ESI ceramic gas nozzle Refer to the topic Cleaning the ESI Insert and Ceramic Gas Nozzle in the chapter Routine and Preventative Maintenance Dirty probe interior Clean the probe interior Refer to the topic The Probe in the chapter Routine and Preventative Maintenance Dirty ESI insert Clean the ESI insert Refer to the topic Cleaning the ESI Insert and Ceramic Gas Nozzle in the chapter Routine and Preventative Maintenance Incorrect probe alignment Align the probe using the procedure on page No signal Loss of high voltage the Probe kV or Corona kV readback is zero in the Tune window Check either the ESI or APCI high voltage electrical connection as Sc MN see and In ESI mode check fo
80. ed The four most commonly used in LC MS applications are shown in Table 6 10 Table 6 10 PEEK tubing color coding Color OD x ID Max pressure Orange 1 16 x 0 020 6000 psig Blue 1 16 x 0 010 6000 psig Yellow 1 16 x 0 007 8000 psig Red 1 16 x 0 005 8000 psig 6 24 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Thermo 2uest Troubleshooting HPLC System Troubleshooting The choice of ID depends mainly on the LC flow In general avoid the red 0 005 ID tubing as it is prone to blockage It is mostly used only for low flow that is lt 100 uL min applications Yellow 0 007 and blue 0 010 are most commonly used for flow rates within the range of typical LC MS applications that is 100 uL min to 1 5 mL min Cut PEEK tubing with a PEEK tubing cutter or scalpel to ensure a square cut and no blockage Flush Peek tubing with solvent before use PEEK fittings used with PEEK tubing are one or two piece with ferrule finger tight compression fittings Never over tighten PEEK fittings as this can cause leaks Stainless steel fittings can also be used but exercise care not to over tighten as the tubing can become crushed and the flow restricted Injection Valves Rheodyne and Valco manufacture the most commonly used injection valves They can be used manually or as part of an autosampler system The injectors can be fitted with
81. emical structure of salbutamol 41 molecular weight 239 e al koa a f l L i wre S E iti ii M wt uon Hh m z 60 80 100 120 140 160 180 200 220 240 260 280 300 Figure 1 8 Electrospray mass spectrum of salbutamol in positive ion mode The base peak at m z 240 see corresponds to the protonated salbutamol molecule It is notable that ESI results in a prominent base peak with minimal fragmentation quite dissimilar from the results often achieved with GC MS Mechanism of lon Generation Electrospray ionization operates by the process of emission of ions from a droplet into the gas phase a process termed Ion Evaporation A solvent is pumped through a stainless steel insert capillary that carries a high potential typically 3 to 5 kV see Figure 1 9 The strong electric field generated by this potential causes the solvent to be sprayed from the end of the insert capillary hence electrospray producing highly charged droplets As the solvent is removed by the desolvation process the charge density on the surface of the droplets increases until the Rayleigh limit is exceeded after which a multitude of smaller droplets are formed by coulombic explosion This process is repeated until charged sample ions remain These ions are then available for sampling by the ion source d AE p A atto A e domm qu o p x uU gt B t Fit o t t t Y p Insert capillary 3 5 kV Droplet As the droplet lons evaporate containing
82. er of ways to measure the amount of liquid flowing into the source and hence measure the split ratio Two methods are provided here one giving a rough estimate and the other a more accurate figure Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ LC MS and AQA Flow FINNIGAN AQA Flow Splitting To achieve a rough estimate of the flow rate into the source 1 Remove the insert from the source enclosure 2 Connect the insert directly to the column outlet and set the flow rate of the LC pump to the desired flow rate into the source for example 0 2 mL min 3 Count the drops that fall off the end of the insert in one minute Make a note of this figure 4 Connect the split as shown in Figure 3 7 5 Now set the LC pump to the flow rate that is required through the column for example 1 0 mL min 6 Count the drops that fall off the end of the insert in one minute If the split is set up correctly in this case to give a split ratio of 4 1 then the number of drops recorded will be the same as that in step 3 If the number of drops is greater than before shorten the length of the tubing connected to the waste or UV detector stream If there are too few drops then a longer length of tubing is required Continue this until the number of drops is the same as that recorded in step 3 Note There is no need to measure the split ratio accurately Even significant changes in sp
83. ert 6 Wipe the now exposed surface of the stainless steel insert capillary with 50 50 methanol water 7 Sonicate the ceramic jet insulator and ESI ceramic gas nozzle in concentrated nitric acid Then boil them in distilled water for 5 to 10 minutes 5 4 Finnigan AQA Hardware Manual ThermoCOuest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Thermo 2uest Routine and Preventive Maintenance The Electrospray and APCI Inserts WARNING Exercise extreme caution when using concentrated nitric acid Always wear protective clothing and use only in a fume hood Observe appropriate disposal requirements when discarding the used acid Replacing the Inserts Replace the inserts if either of them has become blocked or partially blocked during operation A significant increase in LC pump backpressure that is up to 300 psig at 1 mL min added to the total LC system backpressure or instability in the signal could be symptoms of a partially blocked insert Follow steps 1 4 of Cleaning the ESI Insert on page 5 3 to remove the ESI insert or steps 2 4 to remove the APCI insert Alternatively refer to the chapter Changing Ionization Modes Fit a new ESI insert P N 9227 66 or APCI insert P N 9227 65 into the probe and complete steps 1 3 in reverse to secure in place Alternatively refer to the chapter Changing Ionization Modes Finnigan AQA Hardware Manual 5 5 TE Page Search Manuals
84. esolving Common Problems 6 3 Resolving Common Problems The following pages describe how to resolve some of the more easily handled problems Checking Finnigan AQA Power Supply Requirements The Finnigan AQA should be connected to a suitable power supply Full details of the power requirements for your Finnigan AQA MS detector can be found in the Finnigan AQA Preinstallation Requirements Guide Note For details of the power requirements of other system peripherals refer to the appropriate manufacturer s specifications Rebooting the PC Most communication problems that occur with Xcalibur are transient and can be resolved by rebooting the PC To reboot the PC do the following 1 Try to save any open data files Depending upon the nature of the problem this may not be possible Note that any data that is not saved will be lost 2 Close Xcalibur Exit from the Windows operating system in the usual way and switch off the PC Consult your PC user documentation for details 4 Restart the PC the operating system and then Xcalibur Finnigan AQA Hardware Manual 6 19 TTE Page Search Manuals Feedback web Troubleshooting Resolving Common Problems FINNIGAN AQA 6 20 Running Finnigan AQA Tuning Diagnostics In the event of any tuning or calibration problems use the Finnigan AQA tuning diagnostics facility to help identify the nature of the problem To run the tuning diagnostics 1 Cl
85. ess polar than electrospray and of molecular weight lt 1000 amu Typical APCI applications are pesticides drugs azo dyes and steroids A summary comparing electrospray and APCI is shown in able 1 2 Finnigan AQA Hardware Manual 1 23 Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AG Table 1 2 Comparison of ESI and APCI LC MS technique Electrospray ESI Atmospheric Pressure Chemical lonization APCI Compound polarity polar some non polar Examples drugs proteins biopolymers pesticides azo dyes drugs oligonucleotides steroids and metabolites agrochemicals and pesticides steroids Sensitivity fg to pg compound dependent fg to pg compound dependent Type of spectra M H for ve ion mode M H for M H for ve ion mode M H for ve ion mode fragmentation via ve ion mode fragmentation via source voltage source voltage 2 0 uL min to 2 0 mL min 0 2 to 2 0 mL min capillary to 4 6 mm ID columns 2 1 to 4 6 mm ID columns Mobile phases H O CH CN CH OH are most H O CH CN CH OH are most frequently used frequently used Non polar solvents can be used Typical mass range 100 000 1000 1 24 Finnigan AQA Hardware Manual ThermoC2uest TE Page Search Manuals Feedback web FINNIGAN ACXA Thermo 2uest Introducing the Finnigan AQA The Self Cleaning Source AQA Flow 1 4 The Self Cleaning Source AQA Flow This section in
86. f interest lack polar functionalities Points to note e Electrospray is one of the softest ionization methods available whereas APCI although also a soft ionization technique may not be suitable for some very thermally labile compounds as there may be thermal fragmentation see Figure 1 17 1007 214 APCI mass spectrum 4 231 source voltage 25V Electrospray mass spectrum source voltage 25V 0 m z 130 140 150 160 170 180 190 200 210 220 230 240 Figure 1 17 Thermal fragmentation of the herbicide asulam in APCI e APCI does not yield multiply charged ions like electrospray and so is unsuitable for the analysis of high molecular weight compounds such as proteins e Both APCI and electrospray generally provide data from which it is simple to infer molecular weight values In many cases with the correct conditions only one major peak is observed in the spectrum either the protonated molecule M H ve ion or deprotonated molecule M H ve ion However some compounds are more susceptible to fragmentation than others so different degrees of fragmentation may be seen from compound to compound When determining molecular weights always take account of possible adduct ions Common adducts are M 18 NH4 ammonium adducts seen in the presence of buffers such as ammonium acetate M 23 Na sodium adducts and M 39 K potassium adducts Finnigan AQA Hardware Manual ThermoC2uest Manuals
87. f the MS detector to be analyzed This is a unique feature of electrospray Flow Rate The electrospray source can be used with flow rates from 2 0 uL min to 2 0 mL min Finnigan AQA Hardware Manual ThermoC2uest Manuais Page Search Manuals Feedback Web Introducing the Finnigan AQA FINNIGAN AQa The Source an Introduction to API Techniques Atmospheric Pressure Chemical lonization Atmospheric Pressure Chemical Ionization APCD is also a very soft ionization technique and has many similarities to electrospray ionization Ionization takes place at atmospheric pressure and the ions are extracted into the MS detector in the same way as in electrospray Similarly as observed in ESI M H and M H ions are usually formed providing molecular weight information Fragmentation can be induced in the source by increasing the source voltage to give structural information Mechanism of lon Generation In APCI the liquid elutes from an insert capillary surrounded by a coaxial flow of nitrogen nebulizing gas into a heated region The combination of nebulizing gas and heat form an aerosol that evaporates quickly to yield desolvated neutral molecules see Figure 1 12 At the end of the probe is a corona pin held at a high potential typically 2 0 to 3 5 kV This produces a high field corona discharge that causes solvent molecules eluting into the source to be ionized In the atmospheric pressure region surrounding the
88. front end of the probe ensuring that the ESI insert is protruding through the center of the nozzle see Figure 2 4 The nozzle must be fitted in the orientation shown 2 4 Finnigan AQA Hardware Manual 1 ThermoC2uest Manuals Page Search Manuals Feedback web Changing lonization Modes FINNIGAN AQA Setup for ES Corona pin raised into the ESI position Secure corona pin in ESI ceramic ESI insert position using the nut nozzle O O20 XK Figure 2 4 Fitting the ceramic gas nozzle on the end of the probe in the orientation shown and retracting the corona pin 5 Raise the corona pin into the ESI position and secure with the thumb nut 6 Insert the insulated plug P N FM100507 into the ESI position see Figure 2 3 for identification of the insulated plug Thermof 2uest Finnigan AQA Hardware Manual 2 5 TTA Page Search Manuals Feedback web Changing lonization Modes Removal of ESI FINNIGAN AQA 2 4 Removal of ESI The starting point for this procedure is the source setup for ESI operation with the LC and gas flows off and the probe cooled WARNING Allow the source block and probe heater assembly to cool before changing ionization modes Remove the ceramic gas nozzle P N 9227 92 from the front end of the probe see Figure 2 5 ESI ceramic nozzle Figure 2 5 Removing the ESI ceramic gas nozzle 2 Loosen the thumb nut and drop the retaining latch
89. hanol These common reverse phase LC solvents are ideal for LC MS When using high percentages of water the probe temperature usually needs to be raised to aid desolvation in the source Most Compatible Additives The most compatible additives are e Acetic acid or formic acid The LC separations can be enhanced by reducing the pH of the mobile phase Suitable additives for this are acetic acid or formic acid Formic acid is stronger than acetic acid and therefore less needs to be added to reach a required pH Addition of acids can suppress ionization in negative ion analysis and weakly acidic compounds may not form M H ions in acidic conditions e Ammonium hydroxide Ammonium hydroxide ammonia solution is suitable for increasing the pH of the mobile phase which can enhance LC separations When analyzing weakly acidic compounds in negative ion mode it is unlikely that there will be any suppression of ionization Finnigan AQA Hardware Manual 3 3 Manuals Page Search Manuals Feedback Web _ LC MS and AQA Flow LC MS Considerations FINNIGAN AQA e Ammonium acetate or ammonium formate These volatile salts are often used to buffer mobile phases Use as little ammonium acetate or ammonium formate as possible keeping the concentration below 100 mM Ensure that AQA flow is running when using high concentrations e Non volatile salts When using non volatile salts ensure that AQA flow is running as they can
90. he procedure for removing the source and then the procedure for disassembling and cleaning the source if the source has become completely blocked Removing the Source 1 Vent the instrument if it is currently under vacuum Right click on the server and choose Vacuum Vent 2 Remove either the ESI or the APCI insert from the probe If you have been working in ESI mode remember to remove the ceramic gas nozzle from the front end of the probe see 3 Loosen the Swagelok nut and remove the AQA capillary support P N FM100770 from the source If after removing the source you want to remove the hexapole RF lens for cleaning then completely remove this Swagelok fitting P N FM100580 If not the fitting can remain in place Swagelok nut and fitting AQA capillary support Figure 5 5 Loosening the Swagelok nut and removing the AQA capillary support Thermo 2uest Finnigan AQA Hardware Manual 5 7 Manuals Page Search Manuals Feedback web Routine and Preventive Maintenance The Source Block FINNIGAN AQa 4 Disconnect the source voltage connection from the bottom of the source block source block source voltage connection Figure 5 6 Disconnecting the source voltage 5 8 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web Routine and Preventive Maintenance FINNIGAN AQA The Source Block 5 Loosen the thumb screws P N 9227 64 securing the
91. ho Suita City e Osaka 564 0063 e 81 06 6387 6681 Netherlands ThermoQuest BV Druivenstraat 33 NL 4816 KB Breda e 31 076 587 8722 P R China ThermoQuest China Room 912 916 Ping an Mansion e No 23 Jin Rong Street Xi Cheng District e Beijing 100032 e 86 010 6621 0839 Spain ThermoQuest SA e Acer 30 32 Edificio Sertram Planta 2 Modulo 3 ES 08038 Barcelona e 34 093 223 0918 Spain ThermoQuest SA Avenida de Valdelaparra 27 e Edificio Alcor Planta 2a e ES 28108 Alcobendas Madrid 34 091 657 4930 Sweden ThermoQuest AB e Pyramidbacken 3 S 141 75 Kungens Kurva Stockholm e 46 08 680 01 01 Switzerland Spectronex AG Rotterdam Str 21 e Basel e CH 4002 e Switzerland e 41 061 331 6020 United Kingdom ThermoQuest Ltd Paradise e Hemel Hempstead Herts HP2 4TG e 44 01442 233 555 U S A ThermoQuest LC and LC MS Division 355 River Oaks Parkway e San Jose CA 95134 1991 1 408 965 6000 Notes The country code is enclosed in square brackets The city code or area code is enclosed in parenthesis For countries other than the U S A when you are dialing from within the specified country dial the 0 of the city code For countries other than Italy when you are dialing from outside the country do not dial the 0 of the city code Published by Technical Publications ThermoQuest Manchester UK CopyrightO 2000 ThermoQuest Corporation a private subsidiary of Thermo Electr
92. ick on the Start button of the Taskbar and choose Programs Xcalibur Tune to open the Tune window 2 Choose View Diagnostics from the Tune window menu Mnsimmank Diamic BO pleat al er rd iius with then checking DC and sel mass bo mean with zero span wap mass in sepa 1 sactibed RF values Tapori MINAS check F ar n mir max values c i mocisbexd 1 E dini L sea mous an ensuse wollages ma conect polanty Bor we snd ve innizstinn modes LJ Heb Sarin L patom a Calibestion vah coment setings Figure 6 6 Instrument Diagnostics and Optimizations dialog box 3 Select the boxes alongside the diagnostic tests you want to carry out Usually you will need to perform all the diagnostic tests available 4 Click on Start Xcalibur reports the success v or failure x of the tests see ET Finnigan AQA Hardware Manual Thermo 2uest TTE Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Troubleshooting Resolving Common Problems IEESTITTITSTM TET IERI EI REDE check set mass bo ma mih zero span then warp mass in steps checking DC and y s vactibad AF vals tee Setpoint MIM M S chick j ake 3 nun through setpoint seing minima values checking associsted Y Select Al Chew Aill alii es X g Calibuaiec Nor LJ Figure 6 7 Diagnostics results Note You may be asked to run the diagnostics facility should you contact Ther
93. ing down the vacuum light flashes Use the Server to view the Finnigan AQA Properties dialog box pump or vent the system and reset the system Right click on the Server to display a menu e Choose Properties to view the Finnigan AQA Properties dialog box ADA Properties Vacuum gt La j Gas lt Operate Gas gt ESI AQA is in standby Figure 1 24 The Finnigan AQA Properties dialog box e Choose Vacuum Pump to pump down the Finnigan AQA or Vacuum Vent to vent the Finnigan AQA e Choose Reset to reset the Finnigan AQA s communications e Choose Exit to close the server This will be possible only if Xcalibur is no longer running Raw Data Xcalibur acquires data in a raw file Raw data can be viewed as chromatograms and mass spectra see Figure 1 25 The term mass spectrum refers to a plot of mass to charge ratio m z versus relative abundance information The mass spectrum at a particular time in an analytical run will reveal a snapshot of the data at that time The chromatogram is a plot of relative abundance versus time Xcalibur produces the following types of chromatograms total ion current TIC chromatogram base peak chromatogram mass range chromatogram and analog UV chromatogram Thermo 2uest Finnigan AQA Hardware Manual 1 33 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Data System FINNIGAN AG RT 109
94. ing figure 1 21 introduction 1 20 source fragmentation Note 1 21 spares 8 5 spectrum 1 33 status light panel 1 5 figure 1 5 indications table 1 6 stick spectrum 1 35 sulfuric acid 3 5 surface active agents 3 4 T tetrahydrofuran THF use 3 5 use Caution 3 5 thermal fragmentation figure 1 22 TIC chromatogram 1 33 total ion current chromatogram See TIC chromatogram triethylamine TEA 3 5 trifluoroacetic acid TFA 1 1 3 5 troubleshooting APCI high voltage connection location figure 6 9 calibration problems 6 14 calibration problems Note 6 15 calibration problems table 6 14 communication problems 6 16 communication problems table 6 16 ESI high voltage connection location figure 6 9 general problems 6 3 general problems table 6 3 heater and thermocouple wires location figure 6 9 inlet system chromatography problems 6 11 inlet system chromatography problems table 6 11 low sensitivity problems 6 5 low sensitivity problems table 6 5 MS resolution problems 6 18 MS resolution problems table 6 18 probe alignment procedure 6 10 source voltage connection location figure 6 9 spectral problems 6 13 spectral problems table 6 13 tuing problems Note 6 15 tuning problems 6 15 tuning problems table 6 15 vacuum problems 6 17 vacuum problems table 6 17 Thermo 2uest Finnigan AQA Hardware Manual tubing PEEK 6 24 PEEK color coding table 6
95. innigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web LC MS and AQA Flow FINNIGAN AQA Setting up AQA Flow 5 Loosen the Swagelok nut on the top of the reservoir support Insert AQA fused silica capillary P N FM100772 through the Swagelok nut until it reaches the bottom of the reservoir Mark this point with correction fluid 6 Raise the capillary 1 2 mm measuring the distance using the correction fluid mark Tighten the Swagelok nut AQA fused silica capillary Figure 3 3 Installing the AQA fused silica capillary in the reservoir Thermof 2uest Finnigan AQA Hardware Manual 3 9 TTA Page Search Manuals Feedback web LC MS and AQA Flow Setting up AQA Flow FINNIGAN AG 7 Insert the other end of the capillary into the source through the Swagelok nut on the top of the source enclosure 8 Feedthe capillary through this nut and down the AQA capillary support until it touches the edge of the entrance cone orifice Insert the AQA capillary into the source AQA fused silica capillary Move the AQA capillary support into place Figure 3 4 Installing the AQA capillary in the source 9 Tighten the Swagelok nut to hold the capillary in place 3 10 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web LC MS and AQA Flow FINNIGAN AQA Setting up AQA Flow 10 Pull out the mini regulator adjuster in the nitrogen line and turn
96. instrument see page and disassembled see page into its component parts for cleaning WARNING Allow the source block and probe heater assembly to cool before carrying out any maintenance Cleaning the Hexapole RF Lens This procedure only needs to be carried out approximately once every 3 to 6 months under normal working conditions Refer to the Maintenance Schedule topic on page Removing the RF Hexapole Note Follow the procedure for removing the source see page 5 7 before removing the hexapole to carry out maintenance 1 Disconnect the voltage connection to the corona pin voltage connection coron pin Figure 5 12 Disconnecting the corona pin voltage connection 5 14 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA Routine and Preventive Maintenance The Hexapole RF Lens ThermoC2uest 2 Remove the three screws that secure the probe cover plate in position cover plate screws Figure 5 13 Removing the probe cover screws 3 Remove the probe cover plate and corona pin as one item 4 Remove the vacuum line elbow P N 9227 120 o ring P N 5711013 and the Tygon tube P N 9227 123 from the source as a single item o ring vacuum line elbow Figure 5 14 Removing the vacuum line elbow and Tygon tube Finnigan AQA Hardware Manual 5 15 TTA Page Search Manuals Feedback web Routine and Preventiv
97. ion the signal can then be enhanced The real time spectrum can be viewed and the acquisition stopped when the required results are obtained MCA is often used to acquire raw data from the infusion of proteins and peptides 100 oe 893 808 942 771 o 998 738 1060 3 9 44 T 1131 LL Va 1212 0 add W T m z 700 800 900 1000 1100 1200 1300 Figure 1 28 Full scan MCA spectrum of horse heart myoglobin Thermo 2uest Finnigan AQA Hardware Manual 1 37 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Data System FINNIGAN AQA 1 38 SIM Mode This acquisition mode is used when only one or a few specific masses are to be monitored during the acquisition Since most of the acquisition time is spent on these masses the SIM technique is far more sensitive typically greater than a factor of ten than full scan techniques However this sensitivity does depend on the number of masses being monitored simultaneously SIM is also a highly selective technique Impurities present in the sample that co elute with the compound of interest will not affect the analysis as long as they do not produce ions at the same m z value being monitored SIM does not produce spectra that can be used for library searching routines Finnigan AQA Hardware Manual ThermoC2uest Chapter 2 Changing lonization Modes ThermoC2uest Finnigan
98. is listed below In addition to the individual parts this kit contains two additional kits These are e O ring kit part number FM101065 e Screw and fixing kit part number FM101066 Consumables Kit FM100970 Part description Part number Number of each Part category part contained in the kit Source and Hexapole parts hexapole stud springs FM100216 thumb nut for corona discharge pin FM100491 consumable assembly insulated plug FM100507 PEEK zero dead volume ZDV union FM100510 connects the LC tubing or sample infusion capillary to ESI APCI insert corona discharge pin assembly corona 9227 90 consumable pin and connector ceramic jet location nozzle ESI 9227 92 Tygon adapter tube from vacuum line 9227 123 consumable elbow source enclosure seal 9227 125 consumable 6 mm blanking plug underside of 6171001 consumable source enclosure 8 2 Finnigan AQA Hardware Manual ThermoC2uest Consumables and Spares FINNIGAN AQA Cons nahles Part description Part number Number of each Part category part contained in the kit AQA pneumatic parts AQA fused silica capillary FM100772 1 sample infusion fused silica capillary FM100786 graphatized vespel ferrule for Swagelok 6070116 PS ee fittings Rotary pump parts Ultragrade 19 pump oil 4 liters FM101067 foreline trap activated alumina pellets 6060116 14 consumable Source O Ring Kit FM101065 Part description Part number
99. isrupter pin O Entrance cone 89 Zon flow From HPLC o N Orthogonal sample introduction probe Figure 1 7 Schematic of the Finnigan AQA source showing the self cleaning AQA flow Two types of API are commonly encountered These are Electrospray Ionization ESI and Atmospheric Pressure Chemical Ionization APCI The following sections discuss the mechanism of ion generation in each Electrospray Electrospray Ionization ESI is regarded as a soft ionization technique providing a sensitive means of analyzing a wide range of polar molecules Since the first combined ESI LC MS results were announced in 1984 and its first application to protein analysis four years later the technique has become an established analytical tool in separation science Electrospray ionization applied to smaller molecules up to 1000 Daltons in molecular mass results in either a protonated M H see or deprotonated M H molecule Choice of ionization mode is governed by the functional chemistry of the molecule under investigation In ESI fragmentation is generally not apparent however increased source voltages can induce fragmentation to provide structural information Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Thermo 2uest Introducing the Finnigan AQA The Source an Introduction to API Techniques 10 240 OH NH tBu HO HO Ch
100. ite ec ert tege tertie tegere su doped ee e bed Urb EE R laste 8 2 Consumables Kit FM100970 cccecccesssccesscecesneceesaeceeaeeceaceeesaeeeeaaeceeneeceeeeeaeceeaaeceeaees 8 2 8 3 CSparesicosneois E A uses cece tuer etc heirs ies redis 8 5 iv Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ ThermoC2uest Read This First Welcome to the Finnigan AQA LC MS system The Finnigan AQA Hardware Manual provides you with a complete description of the Finnigan AQA MS detector and its operation It includes step by step instructions on changing ionization modes setting up AQA flow and the sample infusion system and routine maintenance procedures Note The information contained within this manual can also be applied to the Navigator with AGA mass spectrometer However the reader should be aware that all text examples and Figures refer only to the Finnigan AQA for the purpose of simplification The Finnigan AQA Hardware Manual includes the following chapters Chapter 1 Introducing the Finnigan AQA provides an overview of each part of the Finnigan AQA MS detector This includes the ionization modes the source the mass analyzer and detector the sample infusion system AQA flow and the data system Chapter 2 Changing Ionization Modes describes how to change the ionization mode that is removing the existing ionization mode and setting up a new one Chapter 3 LC MS and
101. k web FINNIGAN ACXA ThermoC2uest LC MS and AQA Flow Introduction 3 1 Introduction Historically LC MS has only been compatible with volatile buffer systems using modifiers such as trifluoroacetic acid formic acid and acetic acid Phosphate buffers although extensively used in LC separations were not suited to LC MS due to the rapid blocking of the ion sampling region caused by the deposition of involatile phosphate salts The self cleaning AQA API source allows routine LC MS with chromatographic buffers such as phosphates or ion pairing agents and samples in dirty matrices This chapter contains the following information e Details of HPLC solvents and mobile phase additives that focus on LC MS applications using the Finnigan AQA e Instructions on how to setup AQA flow and information on when to use it e Instructions on flow splitting for use with hyphenated detection applications Finnigan AQA Hardware Manual 3 1 Manuals Page Search Manuals Feedback Web _ LC MS and AQA Flow LC MS Considerations FINNIGAN AQA 3 2 LC MS Considerations This section discusses the considerations to be taken into account when choosing solvents and additives and gives guidance on how to optimize LC MS analyses using the Finnigan AQA to produce high quality data Flow Rates In general the column employed determines the choice of flow rate Each column has an optimum flow rate The guidelines in Table 3
102. lit ratio have only minimal effect on chromatographic peak shape To accurately measure the split and therefore know the exact flow rate into the source use the following method 1 Remove the insert from the source enclosure 2 Connect the split to the insert and LC pump as shown in 3 Setthe flow rate of the pump to the flow required through the column for example 1 0 mL min B Collect and weigh the liquid that emerges from the insert in one minute d Follow the same procedure with the liquid that emerges from the waste or UV detector stream 6 Calculate the ratio of the two masses of the liquid to give the split ratio and hence calculate the exact flow rate into the source For example if 200 mg emerges from the insert and 800 mg from the waste stream in one minute then the split ratio is 4 1 and the flow rate into the source can be calculated as 0 2 mL min Thermo 2uest Finnigan AQA Hardware Manual 3 13 TE Page Search Manuals Feedback web LC MS and AQA Flow Flow Splitting FINNIGAN AG 3 14 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ Chapter 4 AQA Sample Infusion System Contents 1 Introduction Overview 3 Setting up the AQA Sample Infusion System ThermoC2uest Finnigan AQA Hardware Manual 4 i TE Page Search Manuals Feedback web AQA Sample Infusion System Introduction FINNIGAN AG
103. luoroacetic acid TFA gt 0 1 v v surfactants Negative ion Surfactants organic acids for example acetic acid formic acid trifluoroacetic acid TFA Use Positive ion Acetic acid formic acid ammonium acetate lt 0 1M Negative ion Triethylamine TEA ammonium hydroxide ammonia solution ammonium acetate lt 0 1M 3 6 Finnigan AQA Hardware Manual Thermo 2uest TA Page Search Manuals Feedback web LC MS and AQA Flow FINNIGAN AQA Setting up AQA Flow 3 3 Setting up AQA Flow Use the following information in conjunction with the setup and maintenance animations on the Finnigan AQA CD shipped with the instrument Note Itis necessary to use the AQA flow system only for dirty matrices or with involatile buffers Choose the AQA flow solvent to give the most effective solubility for the expected contaminants 1 Unscrew the AQA reservoir from its support Figure 3 1 The AQA reservoir Thermo 2uest Finnigan AQA Hardware Manual 3 7 TTA Page Search Manuals Feedback web LC MS and AQA Flow Setting up AQA Flow FINNIGAN AG 2 Fillthe reservoir to 5 mm from the top with a suitable solvent for example HPLC grade water or an organic solvent such as methanol suitable solvent Figure 3 2 Filling the reservoir 3 Check the integrity of the o ring seal Replace the o ring P N FM100200 if it is damaged 4 Screw the reservoir back into its support 3 8 F
104. m lights on the status light panel on the front of the instrument For further information on the status light panel refer to the topic Exterior Features of the Finnigan AQA in the chapter Introducing the Finnigan AQA Finnigan AQA Hardware Manual 7 5 TTE Page Search Manuals Feedback web Shutting Down and Restarting the System Restarting the System FINNIGAN AG 7 6 Finnigan AQA Hardware Manual Thermo 2uest Chapter 8 Consumables and Spares ThermoC2uest Finnigan AQA Hardware Manual 8 i TTE Page Search Manuals Feedback web Consumables and Spares Contents FINNIGAN AQa 8 ii Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Consumables and Spares Introduction 8 1 Introduction This chapter lists the parts most commonly used in the course of working with and maintaining your Finnigan AQA The parts are categorized as follows e Consumable Parts Keep a stock of each of these parts as they may need to be replaced frequently e Spare Parts These parts can be ordered as required Finnigan AQA Hardware Manual 8 1 Consumables and Spares Consumables FINNIGAN AQ 8 2 Consumables All the consumables required for the upkeep of your Finnigan AQA are contained in a Consumables Kit The part number for this kit is FM100970 Each individual part contained in the kit
105. moQuest regarding a tuning or calibration problem Finnigan AQA Hardware Manual 6 21 Manuals Page Search Manuals Feedback Web _ Troubleshooting HPLC System Troubleshooting 6 22 FINNIGAN AQA 6 4 HPLC System Troubleshooting This is a general guide to HPLC system troubleshooting For system specific problems consult the manufacturer s manual This section gives advice on appropriate LC conditions and rectifying LC system problems Buffers and Additives In many cases buffers and or other additives are necessary in the mobile phase to modify chromatography The concentration of buffer additive added is critical as the MS performance can be affected An example of this is the addition of acid in negative ion mode This will suppress ionization of weakly acidic compounds Refer to the chapter LC MS and AQA Flow for information on specific solvents and additives Mobile Phase Reservoir The mobile phase reservoir should be an inert container usually glass fitted with a vented cap to keep particulate matter from entering The white frit serves as a gross filter only always use a 0 45 um filter in line to prevent solid particles from entering the MS detector Bubble Problems and Degassing Bubble problems in LC systems result from mixing air saturated solvents Air is generally less soluble in solvent mixtures than in pure solvents and the excess gas leaves the solution as bubbles Bubbles in the LC sys
106. ms Symptom Probable cause Remedy Excessive noise LC pump fluctuations Thoroughly degas all the solvents Purge the pump at a high flow rate using the current solvent If this fails change the solvent to propan 2 ol and purge the pump again Once primed replace with the required solvent system Check and replace the inlet outlet check valves on the pump Solvent contamination Thoroughly clean all solvent bottles Replace old solvents with new clean solvents Injector contamination Flush the injector with clean solvents Check the injector rotor seal for scratches and replace if it is scratched Clean the syringe port with clean solvents Pump contamination Confirm that the solvents are free from contamination see above Flush all pump solvent lines with a series of clean solvents water followed by methanol Thermo 2uest Finnigan AQA Hardware Manual 6 5 Manuals Page Search Manuals Feedback Web Troubleshooting Troubleshooting Tables FINNIGAN AQA Symptom Probable cause Remedy Excessive noise The probe temperature is too See the Finnigan AQA Getting Started continued low for the flow rate manual for information on the correct probe temperature The LC flow rate is too high Reduce the flow rate or use a splitter Refer to the topic Flow Splitting in the chapter LC MS and AQA Flow for information
107. multiply charged ions and so is unsuitable for the analysis of high molecular weight compounds such as proteins or peptides Although a high temperature is applied to the probe most of the heat is used in evaporating the solvent so the thermal effect on the sample is minimal In certain circumstances for example with very thermally labile unstable compounds the heated probe may cause some thermal fragmentation Flow Rate Flow rates of 0 2 to 2 0 mL min can be used with APCI Finnigan AQA Hardware Manual 1 17 Manuais Page Search Manuals Feedback Web Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AG Source Fragmentation Both electrospray and APCI are regarded as soft ionization techniques Ionization generally results in spectra dominated by either the protonated molecule M H positive ion mode or deprotonated molecule M H negative ion mode depending on whether positive or negative ionization mode has been selected Choice of ionization mode is governed by the functional chemistry of the molecule under investigation Source fragmentation can be induced to give additional information on a compound such as diagnostic fragment ions for structural determination or an increased response on a particular confirmatory ion for peak targeting Formation of Diagnostic Fragment lons The Finnigan AQA allows the simultaneous acquisition of MS data at up to four different
108. ns and WARNINGS A Note contains information that can affect the quality of your data In addition notes often contain information that you may need if you are having trouble A Caution contains information necessary to protect your instrument from damage A WARNING describes hazards to human beings Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web Read This First FINNIGAN aQu Typographical Conventions Topic Headings The following headings are used to show the organization of topics within a Chapter 1 Chapter Name 1 1 Second Level Topics Third Level Topics Fourth Level Topics Fifth Level Topics ThermoC2uest Finnigan AQA Hardware Manual xiii TTE Page Search Manuals Feedback web Read This First Reply Card FINNIGAN AQA xiv Reply Card Finnigan AQA manuals contain a Reader Survey card located at the front of each manual A message on the Reader Survey card asks the user to fill out and return the card after he or she has had an opportunity to use the manual The Reader Survey card has two functions Firstly it allows the user to tell ThermoQuest what he or she does and doesn t like about the manual Secondly when the user returns the card he or she is registered and placed on the ThermoQuest mailing list Once registered the user will receive ThermoQuest s newsletter Analytical News and will be notified of events of i
109. nterest such as user meetings Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ Chapter 1 Introducing the Finnigan AQA ThermoC2uest Finnigan AQA Hardware Manual 1 i TTE Page Search Manuals Feedback web Introducing the Finnigan AQA Contents FINNIGAN AG 1 ii Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA FINNIGAN ACXA introduction 1 1 Introduction The Finnigan AQA MS detector has been specifically designed and engineered for liquid chromatographic detection using Atmospheric Pressure Ionization API and Mass Spectrometry MS technology These technologies can provide sensitive and selective detection of organic molecules Interfacing High Performance Liquid Chromatography HPLC or LC and MS provides the separation scientist with one of the most powerful analytical tools available Both LC and MS have developed to a point whereby they represent two of the most important techniques in characterizing and detecting organic compounds Although the potential benefits of interfacing LC to MS have been clearly recognized for many years producing a truly automated connect and use interface has proven to be a challenging task Atmospheric Pressure Ionization API techniques now provide highly sensitive detection using conventional to capillary LC flow rates on
110. o 2uest Finnigan AQA Hardware Manual 4 7 TE Page Search Manuals Feedback web AQA Sample Infusion System Setting up the AQA Sample Infusion System FINNIGAN AG 4 8 Finnigan AQA Hardware Manual ThermoCuest Manuals Page Search Manuals Feedback Web _ Chapter 5 Routine and Preventive Maintenance ThermoC2uest Finnigan AQA Hardware Manual 5 i Manuals Page Search Manuals Feedback web Routine and Preventive Maintenance Conten FINNIGAN ACXA 5 ii Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Routine and Preventive Maintenance Introduction 5 1 Introduction This chapter contains details of how to perform all the user maintenance tasks on the Finnigan AQA both routine and as required Use this information in conjunction with the setup and maintenance animations on the Finnigan AQA CD shipped with the instrument The chapter begins with a maintenance schedule indicating how often you should perform each routine maintenance task The chapter then describes maintenance of the following parts of the Finnigan AQA The electrospray and APCI inserts The source block The hexapole RF lens The probe The rotary pump The rear panel fan filters Finnigan AQA Hardware Manual 5 1 Manuals Page Search Manuals Feedback Web _ Routine and Preventive Maintenance Mainten
111. oard Photo Ionization Detector Photo Multiplier Detector Photo Multiplier Tube part number peak to peak voltage parts per million pounds per square inch gauge random access memory Finnigan AQA Hardware Manual ix Abbreviations Manuais Page Search Manuals Feedback Web _ Head This First FINNIGAN AQA lt Return gt RF RMS ROM RS232 S SCSI SIM solids probe TIC TCP IP Torr u URL V V ac V dc VGA Return key on the terminal keyboard radio frequency root mean square read only memory industry standard for serial communications second small computer system interface selected ion monitoring direct insertion probe total ion current transmission control protocol Internet protocol torr atomic mass unit uniform resource locator volt volts alternating current volts direct current Video Graphics Array width Watt World Wide Web Note Exponents are written as superscripts In the corresponding online Help exponents are written with a caret or with e notation because of design constraints in the online Help For example MS in this manual 105 in this manual Finnigan AQA Hardware Manual MS n in the online Help 10 5 in the online Help ThermoC2uest TE Page Search Manuals Feedback web FINNIGAN AQA ThermoC2uest Read This First Typographical Conventions Typographical Conventions Typographical conventions
112. ole gt Turbomolecular pump mass analyzer 4 lon trajectory incorrect for transmission through the mass analyzer Hexapole gt Turbomolecular pump RF lens T Source exit cone Figure 1 21 Schematic of the Finnigan AQA analyzer and detector Thermo 2uest Finnigan AQA Hardware Manual 1 29 TTE Page Search Manuals Feedback web Introducing the Finnigan AQA The Vacuum System FINNIGAN AQA 1 30 1 7 The Vacuum System The main challenge in interfacing MS with LC is the introduction of a liquid mobile phase at flow rates of up to 2 mL min into a system that operates under vacuum The transition between atmospheric pressure and high vacuum is achieved by using several different stages of pressure controlled by the vacuum system This arrangement effectively removes the mobile phase leaving the analytes to travel as ions through the mass analyzer It is important to remember that an MS detector must be under high vacuum in order to operate In the case of the Finnigan AQA system not all of the MS detector is under high vacuum The ion source is held at atmospheric pressure while the flow focusing region between the entrance and exit cones is held at an intermediate pressure to step down to the high vacuum region in the mass analyzer and detector The intermediate pressure region is pumped by one rotary pump The high vacuum in the mass analyzer and detector region is achieved by using
113. on Corporation All rights reserved Printed in the UK READER SURVEY Finnigan AQA Hardware Manual Revision C P N FM101638 Please help us improve the quality of our documentation by completing and returning this survey Circle one number for each of the statements below Strongly Strongly Agree Agree Neutral Disagree Disagree The manual is well organized 1 2 3 4 5 The manual is clearly written 1 2 3 4 5 The manual contains all the information need 1 2 3 4 5 The instructions are easy to follow 1 2 3 4 5 The instructions are complete 1 2 3 4 5 The technical information is easy to understand 1 2 3 4 5 The figures are helpful 1 2 3 4 5 If you would like to make additional comments please do Attach additional sheets if necessary Customer Registration Card Register now and receive all the privileges associated with being a ThermoQuest Finnigan product user including customer support application reports technical reports and the ThermoQuest Finnigan publication Analytical News MY ORGANIZATION IS Check one only MY PRIMARY APPLICATION IS Check one only Q Commercial for profit lab Q Analytical Q Government lab Q Biomedical Q Hospital Clinic Q Clinical Toxicology Q Industrial Lab Q Energy Q Research Institute Q Environmental Q University College Q Food Agriculture Q Veterinary Q Forensic Toxicology Q Other Q Pharmaceutical Q Research Education JOB
114. perate Off and vent the instrument 2 Elevate the rotary pump to gain access to the drain plug WARNING The rotary pump is a heavy item requiring at least two people to lift and move it safely 3 Place a container under the drain plug on the rotary pump next to the oil level viewing window Remove the oil filler plug marked Oil from the top of the pump m Remove the drain plug from the pump and allow the old oil to drain out until it reaches a trickle Replace the drain plug Fill the pump reservoir up to but not above the upper mark Replace the filler plug Euer eM Pump down the instrument to prepare for operation Note Leave the system pumping for at least half an hour before commencing operation Thermo 2uest Finnigan AQA Hardware Manual 5 23 Manuals Page Search Manuals Feedback Web _ Routine and Preventive Maintenance The Rotary Pump FINNIGAN AQA Replacing the Foreline Trap Pellets The pellets in the foreline trap need to be replaced periodically to help keep the Finnigan AQA in high vacuum Perform this procedure at the same time as an oil change WARNING Wear gloves when handling the pellets Avoid contact with them as they are poisonous and may contain residues from previously analyzed samples Observe appropriate disposal requirements when discarding the used pellets connection on the rear of the AQA connection on the rear of the AQA _ To the SO
115. pole onto the springs and secure the three nuts to hold the hexapole in place on the source flange Note Tighten the nuts until they are just flush with the ends of the studs Ensure that the hexapole is able to move 2 3 mm relative to the source flange tighten the source flange stud nuts so that they are flush with the top of the studs Figure 5 19 Assembling the hexapole 3 Slide the hexapole back into the instrument along the guide rails Resistance will be felt along the last 2 3 mm Push the hexapole into place with the source flange and secure with two screws Thermo 2uest Finnigan AQA Hardware Manual 5 19 Manuals Page Search Manuals Feedback Web Routine and Preventive Maintenance The Probe FINNIGAN ACXA 5 6 The Probe The inside of the probe can be cleaned This procedure needs to be carried out BED every 6 months Refer to the Maintenance Schedule table on page WARNING Allow the probe heater assembly to cool before carrying out any maintenance Remove the insert from the probe Refer to the chapter Changing Ionization Modes for information on removing the insert 2 Clean the inside of the probe using a cotton bud Q tip soaked in 50 50 methanol water 5 20 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web FINNIGAN AQA Thermo 2uest Routine and Preventive Maintenance The Rotary Pump 5 The Rotary Pump
116. ps to focus the ions before they enter the mass analyzer region Note The source chamber flow disrupter pin and cones are all at the same electric potential which forms a field free region within the source 1 12 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web FINNIGAN AQA Thermo 2uest Introducing the Finnigan AQA The Source an Introduction to API Techniques High Vacuum Region lil vA Intermediate L Rotary Pressure pump Region Flow disrupter pin Flow focusing region Entrance cone OA flow Probe T Atmospheric Ce ee Pressure Insert capillary iine egion Nebulizing gas N Sheath gas N Insert Figure 1 10 Schematic of the AQA ESI source on the Finnigan AQA showing the principal components and pressure regions Spectral Characteristics Polar compounds of low molecular weight lt 1000 amu typically form singly charged ions by the loss or gain of a proton Basic compounds for example amines can form a protonated molecule M H which can be analyzed in positive ion mode to give a peak at m z M 1 Acidic compounds for example sulphonic acids can form a deprotonated molecule M H which can be analyzed in negative ion mode to give a peak at m z M 1 As electrospray is a very soft ionization technique there is usually little or no fragmentation and the spectrum contains only the protonated or dep
117. r excessive condensation in the source enclosure Dry the inside of the source enclosure Ensure that the probe temperature is high enough for the flow rate and that the source enclosure is hot before starting the flow In ESI mode check that the ESI insert is fitted In APCI mode check that the corona discharge pin is positioned correctly Liquid leaks Check all LC couplings Tighten any loose fittings and replace them if defective Replace tubing if appropriate Nebulizer sheath gas leaks Isolate the source of the leak Tighten any loose fittings and replace them if defective No nitrogen gas flow Check the cylinder pressure Check gas supply tubing for leaks 6 8 Finnigan AQA Hardware Manual Thermo 2uest TA Page Search Manuals Feedback web FINNIGAN ACXA ThermoC2uest Troubleshooting Troubleshooting Tables ESI high voltage connection Figure 6 1 The location of the ESI high voltage connection APCI high voltage connection to corona discharge pin Source voltage connection Figure 6 2 The location of the APCI high voltage connection and source voltage connection Probe thermocouple and heater wires Figure 6 3 The location of the probe thermocouple and heater wires Finnigan AQA Hardware Manual 6 9 Manuals Page Search Manuals Feedback Web _ Troubleshooting Troubleshooting Tables FINNIGAN AG Alignment of
118. ripe PEEK tubing Caution Exercise care when handling the APCI insert because it is fragile and may be damaged easily APCI insert thumb nut insert retaining latch Figure 2 1 Removing the APCI insert 2 2 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ Changing lonization Modes FINNIGAN AQA Setup for ESI 2 3 Setup for ESI The starting point for this procedure is a probe with no insert installed WARNING Allow the source block and probe heater assembly to cool before changing ionization modes 1 Fit the ESI insert P N 9227 66 into the probe Caution Exercise care when handling the ESI insert because it is fragile and may be damaged easily ceramic jet insulator 8 blue stripe PEEK tubing Figure 2 2 ESI insert 2 Secure the blue stripe PEEK tubing of the ESI insert to the PEEK union at the inside edge of the source housing using the PEEK finger tight fitting Thermo 2uest Finnigan AQA Hardware Manual 2 3 TTA Page Search Manuals Feedback web Changing lonization Modes Setup for ESI FINNIGAN AG ESI insert insert retaining latch insulated plug Figure 2 3 Installing the ESI insert and securing with the retaining latch 3 To hold the insert in place secure the retaining latch using the thumb nut use finger tight pressure 4 Place the ceramic gas nozzle P N 9227 92 on the
119. ripped down and cleaned Replace the inserts if they become blocked Flushing the Inserts To prevent blockage flush the inserts with 50 50 acetonitrile water or methanol water after use with phosphates ion pairing agents acids or other additives Flush the inserts outside the source enclosure Note To prevent blockage flush each insert after using buffers Cleaning the ESI Insert and Ceramic Gas Nozzle The ESI insert can be stripped down for thorough cleaning after prolonged use with additives Also clean the ESI ceramic gas nozzle 1 Remove the ceramic gas nozzle P N 9227 92 from the front end of the probe ESI ceramic nozzle Figure 5 1 Removing the ESI ceramic gas nozzle Finnigan AQA Hardware Manual 5 3 Manuals Page Search Manuals Feedback web Routine and Preventive Maintenance The Electrospray and APCI Inserts FINNIGAN AG 2 Loosen the thumb nut and drop the retaining latch to the open position Unscrew and remove the PEEK finger tight fitting from the PEEK union at the inside edge of the source enclosure 4 Remove the ESI insert P N 9227 66 and its connecting blue stripe PEEK tubing ESI insert thumb nut insert retaining latch Figure 5 2 Removing the insert from the probe 5 Carefully pull the outer ceramic jet insulator P N 9227 70 to remove it from the insert ceramic jet insulator 5 blue stripe PEEK tubing Figure 5 3 ESI ins
120. roduction 6 1 Introduction This chapter helps you to diagnose and resolve problems that may occur from time to time with the Finnigan AQA LC MS system If you encounter a problem that is not described here or have a problem that is not resolved by the remedy suggested contact your local ThermoQuest service representative who will be able to provide additional advice This chapter is divided into the following sections e Troubleshooting Tables The tables help to identify the precise nature of the problem and the action to be taken e Resolving Common Problems This section provides procedures to help remedy some of the more easily resolved problems you might encounter e HPLC System Troubleshooting This section provides a general guide to HPLC system troubleshooting Finnigan AQA Hardware Manual 6 1 TTE Page Search Manuals Feedback web Troubleshooting Troubleshooting Tables FINNIGAN AQA 6 2 Troubleshooting Tables The tables that follow are designed to help you identify problems in the following areas General system problems Problems relating to the basic operation of the system including for example breaks in power supply Low sensitivity Problems relating to low sensitivity The symptoms are divided into excessive noise low signal and no signal Inlet system chromatography Problems relating to liquid chromatography and the HPLC system Spectral problems Problems rel
121. roperty and so can exist only as an integer that is 1 2 3 and so on The unit of charge used here z is that which is on an electron negative or a proton positive Therefore the mass to charge ratio measured can be denoted by m z Most ions encountered in mass detection have just one charge In this case the mass to charge ratio is often spoken of as the mass of the ion Finnigan AQA Hardware Manual ThermoC2uest TTA Page Search Manuals Feedback web FINNIGAN ACXA Introducing the Finnigan AQA System Overview status light panel ThermoC2uest Exterior Features of the Finnigan AQA This section highlights the exterior features of the Finnigan AQA The parts labeled here may be referred to in later chapters of this manual or other manuals supplied with the Finnigan AQA Figure 1 3 Front view of the Finnigan AQA Figure 1 3 hows the front view of the Finnigan AQA The main feature is the status light panel vent Source open vacuum operate Figure 1 4 The Finnigan AQA status light panel The status light panel shown in gives an indication of the status of the instrument The panel consists of four lights vent source open vacuum and operate Finnigan AQA Hardware Manual 1 5 Introducing the Finnigan AQA System Overview FINNIGAN AG Table 1 1 Instrument status lights instrument status Vent light Source Open Vacuum light Operate light light ven
122. rotonated molecule Some compounds are susceptible to adduct formation if ionization takes place in the presence of contamination or additives such as ammonium or sodium ions The spectra will show other ions in addition to or instead of the quasi molecular ion Common adducts are ammonium ions NH M 18 sodium ions Na M 23 and potassium ions K M 39 Finnigan AQA Hardware Manual 1 13 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AG 1001 322 M H sil M Na 344 80 MP 7 T N 141 145 18 487 261 S282 0 a r I TTT m z 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 Figure 1 11 Electrospray spectrum showing a sodium adduct The singly charged ions arising from samples of relatively low molecular masses can be interpreted directly as they represent the protonated or deprotonated molecule Electrospray however can produce multiply charged ions for analytes that contain multiple basic or acidic sites for example proteins and peptides As an MS detector measures mass to charge ratio m z these ions appear at a m z value given by the mass of their protonated molecule divided by the number of charges E m z n Where M actual mass n number of charges and H mass of a proton Electrospray allows molecules with molecular weights greater than the mass range o
123. roubleshooting vacuum problems Symptom Probable cause Remedy The instrument is either The rotary pump oil level is low Fill the rotary pump with oil Refer to pumping slowly or not the topic Rotary Pump pumping at all Maintenance in the chapter Routine and Preventative Maintenance The foreline trap pellets are Replace the pellets Refer to the saturated topic Rotary Pump Maintenance in the chapter Routine and Preventative Maintenance The rotary pump requires gas Refer to the manual supplied with ballasting the rotary pump Note that under normal operation gas ballasting of the rotary pump is not necessary There is a leak at the vacuum line Vent the instrument Check that the elbow source block or Tygon elbow is seated correctly on the side tube connection of the source block Check the positioning of the Tygon tubing and replace it if necessary Refer to the topic The Source Block in the chapter Routine and Preventative Maintenance Thermo 2uest Finnigan AQA Hardware Manual 6 17 Troubleshooting Troubleshooting Tables FINNIGAN AQA Symptom Probable cause Remedy The instrument is either pumping slowly or not pumping at all continued The flow disrupter pin is missing Replace the flow disrupter pin The flow disrupter pin o ring is missing or damaged Replace the o ring A source block o ring s is missing or damaged Replace the o ring
124. s are the primary reasons for pump seal wear and check valve problems If a buffer has been used flush the pump with clean degassed solvents for example 50 50 methanol water to remove any traces of buffer Ensure the mobile phase reservoir is clean and capped and mobile phase filtered if necessary to minimize the solid particles which may be transferred to the pumping system Change pump seals at least once a year When seals are replaced rinse the piston s to remove any foreign matter inspect it for scratches which will cause future wear and lubricate it by wetting with water or methanol before sliding the pump head and seal back in place To avoid bacterial growth never leave mobile phases containing greater than 70 water in the LC system when it is not in use Acetonitrile is an effective antibacterial agent Tubing and Fittings Three types of tubing are commonly used in LC systems Teflon stainless steel and PEEK Teflon Tubing This is sometimes used in low pressure parts of the LC system The sample does not come in contact with these parts Due to oxygen diffusion through the tubing walls it is susceptible to crimps fitting problems and bubbles Thermo 2uest Finnigan AQA Hardware Manual 6 23 Troubleshooting HPLC System Troubleshooting FINNIGAN AG Stainless Steel Tubing This is suitable for any part of the system that is subject to high pressure Problems with stainless steel tubing aris
125. same source voltage corresponds to the same m z value each time Polarity Switching Switching between positive and negative ionization modes in a single analytical run is supported by the Finnigan AQA Rapid polarity switching is a technique that is applied to several important areas of MS analysis for example e Quantitation of different chemistries within the same run In drug metabolism studies certain compounds preferentially ionize in positive ion mode because they may contain a primary amino group Other metabolites are likely to lose a proton and respond in the negative ion mode for example glucuronide metabolites e Rapid screening of unknown analytes for example in combinatorial chemistry If the compound has a carboxylic acid group that is sterically unhindered it is likely that the compound will lose a proton in negative ion mode and not respond in positive ion mode Thermo 2uest Finnigan AQA Hardware Manual 1 21 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Source an Introduction to API Techniques FINNIGAN AQa 1 22 Application of API Techniques Both electrospray and APCI are ideal for on line liquid chromatography detection providing an additional dimension of information With many compounds it is possible to analyze them by both APCI and electrospray It may be difficult to decide which is the more appropriate technique especially when the compounds o
126. sample infusion system components figure 1 28 flow rate Note 1 27 4 2 functional description 1 27 introduction 1 27 4 i probe temperature Note 4 7 setup 4 3 using with APCI figure 4 2 schedule maintenance 5 2 self cleaning source 1 3 1 25 sensitivity problems 6 5 Sequence Setup 1 32 server 1 32 setup APCI 2 8 AQA flow 3 7 ESI 2 8 sample infusion system 4 3 sheath gas 1 12 1 16 shutting down the system in between analytical runs 7 2 two weeks or more 7 3 up to two weeks 7 2 SIM 1 38 singly charged ions 1 13 1 17 sodium adduct mass spectrum figure 1 14 software Xcalibur 1 31 solvents 3 3 source APCI figure 1 16 ESI figure 1 13 field free region Note 1 12 1 16 flow focused 1 3 introduction 1 9 schematic figure 1 10 self cleaning 1 3 source block cleaning Caution 5 13 cleaning Warning 5 6 cleaning procedure 5 7 cleaning the entrance cone 5 6 disassembling and cleaning 5 10 removing 5 7 removing Caution 5 9 source block o rings cleaning Caution 5 13 source enclosure 4 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ FINNIGAN AQA Index APCI high voltage connection location figure 6 9 ESI high voltage connection location figure 6 9 heater and thermocouple wires location figure 6 9 source voltage connection location figure 6 9 source fragmentation 1 18 source voltage ramp
127. se contained in ThermoQuest Corporation s Terms and Conditions the provisions of the Terms and Conditions shall govern Reference to System Configurations and Specifications supersede all previous information and are subject to change without notice Printing History Revision A printed in June 1999 Revision B printed in August 1999 Revision C printed in June 2000 CD ThermoC2uest The products of ThermoQuest are produced under ISO 9001 accredited quality management systems Australia ThermoQuest e P O Box 239 Rydalmeree Unit 20 Metro Centre e 38 46 South Street e Rydalmere N S W 2116 e 61 02 9898 9000 Austria Spectronex GmbH Bischoffgasse 26 e A 1120 Wein e 43 01 813 9993 Belgium ThermoQuest BVBA Groenenbrogerlaan 84 e B 2610 Wilrijk Antwerpen 32 03 825 06 70 Canada ThermoQuest Canada 5716 Coopers Avenue Unit 1 e Mississauga Ontario e L4Z2E8 e 1 905 712 2258 France ThermoQuest France SA Parc Hightec Sud e 12 avenue des Tropiques Z A de Courtaboeuf BP141 e F 91944 Les Ulis C dex e 33 01 69 18 88 10 Germany ThermoQuest Analytische Systeme GmbH e Boschring 12 e D 63329 Egelsbach e 49 06103 408 0 Italy ThermoQuest Italia S p A e Strada Rivoltana I 20090 Rodano Milano e 39 02 95 059 1 Japan ThermoQuest K K e Nishi Shinjuku Toyokuni Building 3rd Floor e 2 5 8 Hatsudai Shibuya ku e Tokyo 151 0061 e 81 03 3372 3001 Japan ThermoQuest K K Esaka Grand Building e 2 3 1 Esaka c
128. seal Higher than normal backpressure on the LC pump Blocked or partially blocked insert Replace the insert Refer to the chapter Changing lonization Modes Lower than normal backpressure on the LC pump Solvent leakage Check for any solvent leaks especially inside the source enclosure Repair or replace any faulty LC couplings 6 12 Finnigan AQA Hardware Manual Thermo 2uest Manuals Page Search Manuals Feedback Web _ Troubleshooting FINNIGAN AQ Troubleshooting Tables Spectral Problems able 6 4 details for each spectral problem the symptom probable cause and remedy Table 6 4 Troubleshooting spectral problems Symptom Probable cause Remedy Missing high mass peaks The scan speed is too fast This will only happen if Advanced mode is selected Reduce the scan speed Clear the Advanced check box on the Acquisition page of the method editor to allow Xcalibur to limit the scan speed The spectra are skewed or distorted The scan speed is too slow Increase the scan speed to give greater than 6 scans across the peak Incorrect isotope peaks ratios LM HM Res settings are incorrect or the ion energy setting is too high see the Tune window Inaccurate calibration The detector is being overloaded Infuse the sample and set the LM HM Res settings and or ion energy for good resolution Re calibrate Refer to the Finnigan AQA
129. ted green off off off venting flashing green off off off pumping down off off flashing green off under vacuum above off off amber off vacuum trip under vacuum ready for off off green off use Operate On Finnigan off off green green AQA in use source enclosure open off flashing amber green amber Operate On source enclosure open off flashing amber green off Operate Off The vacuum trip is the pressure below which it is safe to switch on the voltages in the source When the instrument is functioning normally the vacuum light will go from flashing green to solid green and Operate can be switched On If the pressure in the instrument rises above the operating pressure the vacuum light turns amber to indicate that the pressure is above a safe level See the chapter Shutting Down and Restarting the System for information on pumping down the Finnigan AQA 1 6 Finnigan AQA Hardware Manual ThermoC2uest TTA Page Search Manuals Feedback web Introducing the Finnigan AQA FINNIGAN AQA System Overview Figure 1 5 phows the front view of the Finnigan AQA with the doors open e source enclosure and AQA reservoir are now visible source enclosure AQA reservoir Mil OEE Figure 1 5 Front view of the Finnigan AQA doors open Thermo 2uest Finnigan AQA Hardware Manual 1 7 Manuais Page Search Manuals Feedback Web Introducing the Finnigan AQA System Overview FINNIGAN
130. tem can cause instability in UV and other detectors and in API sources Thorough degassing can minimize bubble problems in the mobile phase Heating is the most efficient way of removing gas from reversed phase solvents but this is inconvenient The most common way of degassing solvents is using a vacuum membrane degasser Many LC systems have this feature Another efficient way to degas solvents is by helium sparging Use a flow of 300 mL min for 3 to 4 minutes and then reduce the flow to a trickle most LC systems allow constant helium sparging One liter of helium can degas one liter of solvent with 99 efficiency Only sparge for a few minutes at high flow to minimize evaporation of mobile phase and potential change in composition Degassing in an ultrasonic bath is a poor technique for removal of gas from solvents Normal phase solvents do not need to be degassed Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback Web _ Troubleshooting FINNIGAN AQa HPLC System Troubleshooting Bubbles trapped in the pump head are also a problem and can be removed by e Flushing the pump with degassed mobile phase try increasing the flow rate to 5 mL min e Opening the purge valve and increasing the flow e Gently tapping the pump head e Washing the system through with methanol or IPA isopropyl alcohol Contamination in the LC System Buffer residues and solid particles from mobile phase
131. tivity Problems on page B Refer to Low Sensitivity Problems on page Contamination of calibration compound Check that the calibrant is free from contamination and within the acceptable storage lifetime Prepare a fresh calibration standard Liquid leakage Check for leaks and repair or replace tubing and fittings as necessary The first peak lowest mass in the acquired spectrum is too weak Alter the calibration range to start with a strong first peak Concentration of the calibration sample is too low Increase the concentration of the calibration sample Using the incorrect reference file Check that the selected reference file relates the calibrant being used Check that the calibration reference file contains the correct masses and reload if necessary Poor sample preparation Refer to Low Sensitivity Problems on page Instability of the liquid spray Refer to Low Sensitivity Problems on page Incorrect default tune values Check the tune page settings for the system voltage settings Poor resolution Check LM HM Res and ion energy settings Masses are drifting Excessive temperature fluctuations High fields Check room temperature Check the operation of the water chiller if this option is fitted and rear panel fans Check for other instruments emitting high fields in close proximity Change instrument location if necessary
132. tom Probable cause Remedy Post column band broadening Poor LC connections Damaged ESI APCI insert Check all couplings between the injector and the detector for bad connections or for tubing that has been incorrectly cut Check the condition of the ESI APCI insert and replace if necessary Peak tailing in APCI Incorrect probe heater temperature Optimize the temperature of the probe heater by a series of loop injections at different temperatures Fluctuating baselines Bubbles in LC system especially in the solvents or pump heads Column failure Thoroughly degas all solvents prior to use Purge the pump to remove trapped bubbles from the pump heads Replace column High TIC Contamination Refer to the topic Low Sensitivity Problems on page Excessive baseline noise High aqueous mobile phase at a high flow Leaking injector rotor seal If the analyte elutes in the region of high aqueous mobile phase increase the probe temperature to maximize the desolvation properties of the source Replace the injector rotor seal Negative peaks in flow injection analysis Poor solvent preparation Leaking injector rotor seal Check the solvent compatibility Check that the samples have been prepared using clean solvents free from contamination Check the solvents used for the mobile phase are clean and free from contamination Replace the injector rotor
133. top of the reservoir support Insert the long sample infusion fused silica capillary P N FM100786 through the Swagelok nut until it reaches the bottom of the sample vial Mark this point on the fused silica with correction fluid 7 Raise the fused silica capillary 1 2 mm measuring the distance using the correction fluid mark Tighten the Swagelok nut sample infusion fused silica capillary Figure 4 3 Installing sample infusion fused silica capillary 4 4 Finnigan AQA Hardware Manual 1 ThermoC2uest Manuals Page Search Manuals Feedback web AQA Sample Infusion System FINNIGAN AQ Setting up the AQA Sample Infusion System 8 If LC tubing is present disconnect it from the PEEK union at the outer edge of the source enclosure Connect the other end of the fused silica capillary to the PEEK union at the outer edge of the source enclosure fused silica sample infusion capillary ESI insert Figure 4 4 Connecting sample infusion capillary to the source enclosure 9 Pull out the mini regulator adjuster in the nitrogen line and turn clockwise to pressurize the AQA reservoir When the regulator reads approximately 6 psig stop turning and push the adjuster into its locked position A reservoir pressure of approximately 6 psig gives a sample infusion flow rate of 10 uL min Figure 4 5 Turning the mini regulator adjuster Thermo 2uest Finnigan AQA Hardware Manual 4 5 Manuals Page Search
134. tor 4 Hexapole l RF lens X Quadrupole mass analyzer Turbomolecular pump Turbomolecular pump Exit cone gt Rotary pump i1 o Eon Flow disrupter pin focusing region Entrance cone N an flow From HPLC gt Orthogonal sample introduction probe Figure 1 2 Schematic diagram of the Finnigan AQA API inlet analyzer and detector system The LC eluent is ionized at the API probe with the resulting ions flow focused into a hexapole RF lens The quadrupole mass analyzer filters the ions before detection Ther mot 2uest Finnigan AQA Hardware Manual 1 3 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA System Overview FINNIGAN AQA What is Mass Detection Mass detection is a very powerful analytical technique used in a number of fields including e Identification of unknown compounds e Quantitation of known compounds e Determination of chemical structure The basic function of an MS detector is to measure the mass to charge ratio of ions The unit of mass used is the Dalton Da One Dalton is equal to 1 12 of the mass of a single atom of carbon 12 This follows the accepted convention that an atom of carbon 12 has exactly 12 atomic mass units amu The MS detector does not directly measure molecular mass but the mass to charge ratio of the ions Electrical charge is a quantized p
135. troduces AQA flow Information on how and when to set up AQA flow is given in the chapter LC MS and AQA Flow Introduction The API source on the Finnigan AQA includes a self cleaning solvent delivery system This makes the source extremely robust and productive greatly increasing the number of samples that can be analyzed routinely before maintenance is required The orthogonal API probe serves to direct the LC eluent away from the inlet orifice However under typical LC MS conditions both the ions and the charged liquid droplets containing involatile components are deflected by the electric field towards the inlet orifice This effect leads to a gradual build up of involatile components and a concomitant loss in sensitivity with time The self cleaning AQA source delivers a constant low flow of solvent to the edge of the inlet orifice see Figure 1 18 This prevents the build up of involatile components during LC MS analysis with typical chromatographic buffers for example phosphates and ion pairing agents Thus AQA greatly improves the quantitation precision of analysis without the need to compromise the LC method and more importantly dramatically extends the length of time possible for analysis Figure 1 18 Dispersion of involatile components from the inlet orifice Finnigan AQA Hardware Manual 1 25 Manuals Page Search Manuals Feedback Web _ Introducing the Finnigan AQA The Self Cleaning Source AQA
136. tting Due to the Finnigan AQA s source design it is not a requirement to use flow splitting of the LC eluent However if hyphenated detection is required flow splitting can be achieved in the following way Zero dead volume T piece HPLC column Fused silica ip to insert a vA W N and source PTFE sleeve ln F PTFE sleeve Fused silica to waste or UV PEEK LC tubing Figure 3 7 Schematic of a split A simple and effective way to make a post column split for use with the Finnigan AQA is shown in 1 Connect a zero dead volume T piece to the exit of the column using the normal PEEK or stainless steel LC tubing PEEK tubing is used in the figure 2 Connect one of the exits of the T piece to the source enclosure using narrow bore PEEK tubing or as shown in the diagram fused silica Use a PTFE or orange stripe PEEK tubing sleeve to secure the fused silica into the T piece 3 Connect a length of the same tubing to the other exit the split stream The amount of liquid directed through the split stream is determined by the back pressure exerted at this exit and hence by the internal diameter and the length of the tubing attached As a general rule the longer the piece of tubing attached to the split the greater the flow to the source and the smaller the split To reduce the flow to the source and increase the split shorten the length of tubing at the split stream exit There are a numb
137. vacuum line clamp P N 9227 118 in position Pull the clamp towards you as far as it can go Disengage the vacuum line elbow P N 9227 120 from the clamp 6 Remove the two screws holding the source block in place P N FM100382 Remove the source block source screws vacuum line clamp thumb screws vacuum line elbow Figure 5 7 Disengaging the vacuum line elbow from the clamp and removing the source screws to allow the source block to be removed Caution Support the source block from below to prevent it from falling Thermo 2uest Finnigan AQA Hardware Manual 5 9 TTE Page Search Manuals Feedback web Routine and Preventive Maintenance The Source Block FINNIGAN aQu Disassembling and Cleaning the Source Block 1 Remove the voltage connection screw P N 5312004 pin P N 9227 113 and washer P N 1150705 from the bottom of the source vacuum clamp thumb screws washer Screw voltage connection pin Figure 5 8 Removing the voltage connection and vacuum line clamp 2 Remove the thumb screws P N 9227 64 and vacuum line clamp P N 9227 118 from the side of the source block 5 10 Finnigan AQA Hardware Manual ThermoC2uest Manuals Page Search Manuals Feedback web Routine and Preventive Maintenance FINNIGAN AQA The Source Block 3 Remove the disrupter pin P N 9227 119 and o ring P N 5711003 o ring disrupter pin Figure 5 9 Removing the disrupter pin and o ring
138. y electrostatic discharge electrospray ionization electron volt femto 10 15 degrees Fahrenheit Flame Ionization Detector Free on Board Flame Photometric Detector foot file transfer protocol gram giga 10 gas chromatograph gas chromatograph mass spectrometer electrical ground general purpose interface bus graphical user interface height hour high performance liquid chromatograph high voltage hertz cycles per second Interactive Chemical Information System Instrument Control Language International Electrotechnical Commission Institute of Electrical and Electronics Engineers inch input output kilo 10 1000 kilo 210 1024 kilogram length Finnigan AQA Hardware Manual Thermo 2uest Manuais Page Search Manuals Feedback Web FINNIGAN AQA ThermoC2uest Head This First Abbreviations LAN LC LC MS LED MS MS MS NCBI NIST Pa PC PCB PID PMD PMT P N P P ppm psig RAM liter local area network pound liquid chromatograph liquid chromatograph mass spectrometer light emitting diode meter milli 10 3 mega 106 molecular ion micro 10 9 minute milliliter millimeter scan power MS scan power MS scan power MS nz 1 through 10 mass to charge ratio nano 10 9 National Center for Biotechnology Information USA National Institute of Standards and Technology ohm pico 10 12 pascal personal computer printed circuit b

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