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USER MANUAL CUBE Microlitre Spectrophotometer

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1. r 3 User Account Control e Windows needs your permission to continue If you started this action continue Jagi Network Connections Microsoft Windows v Details continue Continue I Gen Cancel User Account Control helps stop unauthorized changes to your computer Select Internet Protocol Version 4 TCP IPv4 ensuring that the checkbox to the left of the item remains checked Now click on Properties H Local Area Connection Properties x Connect using Le Broadcom NetXtreme Gigabit Ethemet This connection uses the following items DM Client for Microsoft Networks vi Z Microsoft Network Monitor 3 Driver 4 2 Virtual Machine Network Services v Ji QoS Packet Scheduler v ee Printer pruma Microsoft Networks m intemet Protocol Version 4 TCP IPv4 H Install Uninstall Sune ea DERIN DIR The default HEV za zi rec wez peda iar Ceren rek across diverse interconnected networks Picodrop CUBE User Manual version 1 0 May 2013 Page 39 Enter the values as below and click OK to save changes Make sure that there are no other network adapters active you may need to consult your system s user manual to achieve this You can get IP settings assigned automatically if your network supports this capability Otherwise you need to ask your network administrator for the appropriate IP se
2. Pinging 18 8 8 123 with 32 bytes of data Reply from 10 0 0 123 bytes 32 time lt ims TTL 64 Reply from 10 0 0 123 bytes 32 time lt ims TTL 64 Reply from 10 0 0 123 hytes 32 time lt ims TTL 64 Reply from 10 0 0 123 bytes 32 time lt ims TTL 64 Ping statistics for 10 0 0 123 Packets Sent 4 Received 4 Lost loss Approximate round trip times in milli seconds Minimum ms Maximum ms Average Gms iC Users Astranet gt _ Picodrop CUBE User Manual version 1 0 May 2013 Page 31 e It is critical that there are no lost packets the Lost value must read 0 If the loss is above 0 then the network adapter isn t configured correctly or is disabled or another network adapter is still enabled and responding to requests to 10 0 0 10 Go back over the steps and ensure each action has been followed e An example of the result of the ping command where incorrect network settings are in use Microsoft Windows Version 6 1 7601 Copyright lt c gt 2669 Microsoft Corporation All rights reserved 10 0 0 123 with 32 bytes of data timed out timed out timed out Request timed out Ping statistics for 10 0 0 123 Packets Sent 4 Received Lost 4 100 loss C Users Astranet gt _ e If this test is not successful re check that the correct Ethernet cable has been used and is connected correctly Also ensure that the settings detailed in the installation procedure have been set correctl
3. USER MANUAL KE Picodrop CUBE CUBE Microlitre Spectrophotometer User Manual NOTES CONTENTS CE DECLARATION OF CONFORMITY A 5 ESSENTIAL SAFETY NOTES eee iner yi n nene k n tas kada aba ek k da veda dek B ab da GR aa xa bda y d n n n 6 Potential Safety Hasan S ene dee ea ba E ake Kek bay HE sekan Mire RRR dake E 7 Electteak edel SNE gege ated eee tee ee 7 Hazardous Substances 4 4 kk kake kk kak kK A KAKA KAR KA KAK AA KA KA KAK kK A AA A A AA KA KA A 7 Solvent Compatibility lsa yaye eel ao ake e seein awa rekan e S RA KOR ean ain 7 Instrument case and paintwork EE kek axak kak K k kak k KAK kk AK kK K KA KA KAK 7 INTRO HONN A A ee 8 ELE CIR 8 Principle of Operation 2 id yl l M la kn a a u hi ege deg 8 Measurement Modes Et Eek kk kk kk kek kk kek KAKE KA KAK kk KAK AKA A A KAK KK AA k KAKA KARA 9 Principle of Measurement lk lll Ei kk kek kk kek kk kk kk kek kk K k KAKA kK AA A KA kk KAKA KRA 9 Microsample 3CC S 0D 252 0555549 S055 ETE Zak n AR AZ uan Ek ya Dek 9 User and Data Management 11 INSTALLATIONS zl n nun y k k r k eee shea da ay be he tea bev ee ees 12 UNPackin Gua iit cnn cok a R Ee anita 12 POSITIONING EE 12 Hardware installation if not already pre assembled scccesccecesseeesseeeesseeeessseees 13 Assembling the pipette holder 13 Connecting the fibre optic Cables u kk kk kk kk kk kk kk Ak A KAK
4. e Insert the pipette with sample and press the Measure button e After a few seconds the concentration in ng pl will appear in the bottom right hand window the spectrum will be plotted and details displayed in the table below the graph e It is not necessary to save the results as all results are done so automatically rk a a a aa ae e a Wavelength nm Absorbance A 1cm equivalent Result A260 A280 A260 A230 Path Date Time 26no 110 833 1335 Pipette Tip 0 092cm 09 01 2013 10 24 Delete Export i Clear Overlays Example of results using ssDNA mode e Subsequent measurements are positioned below the previous one Several sets of data can be selected and are then overlaid automatically use Clear Overlays to remove this To delete a set of data highlight using the cursor and select Delete Picodrop CUBE User Manual version 1 0 May 2013 Page 18 Export of data to Excel e Data can be easily exported to Excel for subsequent analysis and normalisation for inclusion in reports etc To do this e Double click on the results of interest e Select the required data interval from 1nm or 0 1nm 1nm should normally be sufficient otherwise the data files will be extremely large e Select the display format for data from Horizontal or Vertical Vertical is usually more manageable e Select the folder to which the data is to be saved and enter a file name e Open Excel and nav
5. May 2013 Internet Protocol TCP IP Properties General You can get IP settings assigned automatically if your network supports this capability Otherwise you need to ask your network administrator for the appropriate IP settings Obtain an IP address automatically IP address j p Subnet mask 8 HZ Default gateway e Use the following DNS server addresses Prefered DNS server Altemate DNS server _Intemet Protocol Version 4 TCPAPv Properties Ea General You can get IF settings assigned automatically if your network supports this capability Otherwise you need to ask your network administrator for the appropriate IP settings Obtain an IP address automatically Use the following IP address IP address Subnet mask Default gateway Obtain DNS server address automatically Use the following DNS server addresses Preferred DNS server Alternate DMS server E Validate settings upon exit Page 41 Setting IP addresses in a Windows 7 8 system Open the Control Panel by pressing the Start button Microsoft flag globe in the bottom left corner of the screen and then selecting Control Panel option in the menu to the right hand side of the start screen below User Name Games Favorites Computer w Microsoft Virtual PC Control Panel Administrative Tools gt Devices and Printers gt All Programs Help and Support Sea
6. lt Indexing Intel Ge Options PROSet Wir j x o NVIDIA Offline Files Parental Control Panel Controls Devices a TI T Printers e Programsand QuickTime wee CN Features Language 8 e be g l Speech Sync Center System TabletPC Taskbar and Text to Recogniti Settings Start Menu Speech ES 1 a KEE Windows Windows Windows eee Mobilit Sidebar SideShow d AS Pen and Input pan Near Performance Personaliza Regional and Saeson Secure Online User Accounts Ov a Bluetooth Devices erage 2 amp L emer iSCSI Initiator Java Re Informati lt AN Key Backup Center sc wy Welcome Windows Center CardSpace Date Ae Time Petes Device Manager 0 Mail sc See and Power Options a e Silicon Image Sound SATA Con Windows Windows Defender Firewall Now select Network and Sharing then select manage network connections from the menu on the left you may need to consult the manual for your computer system to find out which controller to use GU RE Control Panel Network and Sharing Center File Edit View Tools Help Tasks View computers and devices Connect to a network Manage wireless networks Set up a connection or network Pa Diagnose and repair See also Intel PROSet Wireless Tools Internet Options Windows Firewall Network and Sharing Center View full map D A A
7. CUBE User Manual version 1 0 May 2013 Page 26 ACCESSORIES Pipette tips ONLY USE THE PIPETTE AND TIPS SUPPLIED BY THE ORIGINAL EQUIPMENT MANUFACTURER DO NOT USE ALTERNATIVES DO NOT AUTOCLAVE THE TIPS The pipette included with the instrument requires a supply of disposable UV tips These tips are made from a special UV visible transmitting optical grade polymer that is also significantly more dimensionally stable and reproducible than normal tips do not use alternatives These UV pipette tips are available in two forms one which is Raze free and must be used where the sample is to be retained the other which is bulk packed can be used where RNAse free handling is not required Order codes and descriptions are as follows Description 50 boxes x UVT 2xBags of 1 box of 96 RNAse free tips in easy dispense rac RNAse free tips in bulk bag RNAse free tips in easy dispense rack Other CUVO1 Standard pathlength cell holder 10mm For use with other cuvettes 0 5mm 1mm 5mm and 10mm pathlengths can be accommodated including Hellma TRayCell DP317UV Immersion probe with 3 17mm stainless steel barrel Includes 10mm path length tip and connecting UV grade fibre optic cables patch cords not required Picodrop CUBE User Manual version 1 0 May 2013 Page 27 MAINTENANCE Cleaning This spectrophotometer is designed to require a minimum amount of maintenance by the u
8. KAK 13 Connection and loading the software to your bt 15 Minimum specification for the BC 15 APPLIGATION M O DES steet d an kardar ident Ku R dR N a KEK EE OW AKA R KE W VT Be RAKIN 16 Getting Started RRM DDMDMDMNNN N N NIM MM MMMMM MJ Jj AEIuIInnVMDMIIIIMI MMM M 16 Correct pipette use and sample bhandltng kk kek kk kk kk kk 17 Nucleic Acid Measurement Ek kk kk kk KA kA KA KA KA KAK AR kk KA kk KA A KH 18 Export of data to Excel 19 Direct Protein Measurement An 19 Exportiof datato Excel sirrane a aa ria Dek Dak kak ERA R k 20 Picodrop CUBE User Manual version 1 0 May 2013 Page 3 Indirect Protein Measurement ccccecceccsceseececescsseeueusesseaueesesseuaaeseeeeeueeaaaeeeeueeaaes 21 Pull Scano tate devaseces eats rey ieee nae ee ha eer cl a eae eee 24 Oe EEE REP ERCECL EERE ERECT CRECLE LEER a a SE 25 Graph overlay and Normalisation of wavelength background correction 25 Export of data to Excel 25 ACCESSORIES a 2 425 ir ba auaa ereire aea aie Gant eevee Gants 27 NI er de 27 OMEk reta lates A oe E A ene ENE MENA Eren al eae Aeon tatters SN 27 MAINTENANCE aere dee tege date e a e ia evened ers 28 TU e DE 28 Quick Clean procedure for sample holder 28 Troubleshooting EE 28 Power indicator does not Irgbt kk kek kk kk k kk kk ka kk kk kk ka rennan KA 28 Inconsistent Festlee dan dan e ie eee 28 L ns cleaning Liye Lw g ggg mm e yUaVh j 30 Connection Lost MESSAGE spr
9. idris li dan Kak nl nd E ken ka d k TL kek Ayak Gan Wiy gan ka ken aa 31 Communications Error message 31 Ethernet Connection failed Sarsina iian kya V A kena d ya eine ge 31 SPECIFICATIONS eege yaka Yek rika kk bank daa erkek kak y Ke kek ei Neser 33 APPENDIX 1 APPLICATIONS uu Eke kek kk kk kK KAK AKA KAKA KAK KAK AK RA 34 Measuring Nucleic Acid Concentration and Purity uuu uk kk kk kk 34 Protein Measurements scinsioni SEENEN Ker A ke tabi eves Ke W n n ek kek U K R S ake 35 Indirect measurement l llili kek kk kk kk KAKA KAK KARA KK KA KAK KAK KK KK KA KAK AA RA 35 Direct measurement anini ke l n M dai Make Hek N N kin Al Mel ll hein y kan ek 35 Molar Extinction Coefficients vs Absorbances for 1 Solutions 36 Measuring a Protein or Protein Mixture with Unknown Extinction Coefficients 37 APPENDIX 2 SETTING IP ADDRESSES Luke kek kk kk KK KAK AK A KAK KRA KA RA 38 Setting IP addresses in a Windows Vista system 38 Setting IP addresses in a Windows XP system 40 Setting IP addresses in a Windows 7 8 system 42 Picodrop CUBE User Manual version 1 0 May 2013 Page 4 CE DECLARATION OF CONFORMITY Product Optic Coupled Spectrometer Type SWIR NIR VIS NIR UV VIS We declare that the above specified systems are compliant with the regulations of the European Community when installed as a system The devices a
10. time select Settings Current Sampling Accessory Pipette Tip 0 092 cm Increased Precision Mode High precision mode off Sample Storage Folder C Users Astranet Documents Change e Current Sampling Accessory refers to the sample handling containment that will e be routinely used this will usually be pipette tip If it needs to be changed select Change and choose from the choices available Pipette tip 0 5mm 1mm 10mm Other e The descriptions in the following sections assume pipette tips are used if this is not the case the same sequence of actions is still applicable e High precision mode refers to whether the xenon lamp is continuously on or goes e off after a measurement The default is off and this is recommended for most multi user laboratories e Sample Storage folder enables the user to define the default folder to which data e should be saved on the PC or network e Once these have been defined press Close and select the application mode Note that once set there is no need to go back to Settings unless there is a change of modus operandum Picodrop CUBE User Manual version 1 0 May 2013 Page 16 Correct pipette use and sample handling e Vortex sample briefly 5 20secs and then spin down samples briefly 10 15secs in a microphage e Using the supplied pipette and UV pipette tips pipette up your sample A minimum e volume of 2 5ul is recommended To minimize solution on the outside of th
11. tip in a light beam emitted from a fibre optic cable connected to the holder The light source is a pulsed xenon lamp housed in the instrument and the light path through the tip is 1mm Through the Tip Measurement Technology UV Transparent dimensionally stable RNAse free Pipette tip Fibre Optic cable from UV light source Sample is retained inside tip and can be as small as 2jl Fibre Optic cable to polychromator and CCD Array detector The light passes through the sample still retained in the tip and the light transmitted through it is collected by a second fibre optic cable on the opposite side of the holder The transmitted light is then analysed in the polychromator based spectrophotometer also housed in the instrument where the Absorbance Concentration Purity Ratio and other values are calculated The instrument is controlled using the supplied software run from a PC or laptop via an Ethernet connection The pipette tips and pipette holder accessory are all critical components in making accurate and reproducible measurements of micro sample volumes including DNA RNA and Protein measurements The tips are made from a special UV visible transmitting optical grade polymer that is also significantly more dimensionally stable and reproducible than normal tips do not use alternatives ONLY USE THE PIPETTE AND TIPS SUPPLIED BY THE ORIGINAL EQUIPMENT MANUFACTURER DO NOT USE ALTERNATIVES AND DO NOT AUTOCLAVE TIPS For
12. Full Scan Sample name 0 04 583 4nm 10mm Cuvette 1cm 09 01 2013 15 26 Full Scan Sample name 1 11 230 Dm 10mm Cuvette 1cm 09 01 2013 15 34 Full Scan Sample name 0 59 250 Dm 10mm Cuvette 1cm 09 01 2013 16 01 Delete Export Print Clear Overlays Close An example of zooming in on a multiple overlays Normalisation of wavelength background correction A normalisation wavelength to correct for its absorbance value over the whole spectrum and therefore background correction at a specific wavelength can be applied if required This is done by pressing the Enable option and entering the normalisation into the box the spectrum will need to be run again Export of data to Excel Data can be easily exported to Excel for subsequent analysis and normalisation for inclusion in reports etc To do this Double click on the results of interest Select the required data interval from 1nm or 0 1nm 1nm should normally be sufficient n otherwise the data files will be extremely large Select the display format for data from Horizontal or Vertical Vertical is usually more n manageable Select the folder to which the data is to be saved and enter a file name Dpen Excel and navigate to the file in question note that data is exported as a text file LDpen the file it is a text delimited file with tab separation Manipulate that data as appropriate and save in the required format Picodrop
13. Linear Display of calibration standards linear regression To measure samples against this standard curve place the pipette tip containing your protein into the instrument and press Measure the absorbance result is extrapolated to the curve and the corresponding calculation result is displayed e This result should be recorded in a laboratory notebook e Indirect protein sample determination should always be done using freshly prepared standards and not using standard curves prepared previously For this reason results are not available for print out or transfer to spreadsheet Picodrop CUBE User Manual version 1 0 May 2013 Page 23 R 0 998663194125419 Formula Y 7 05023256 66 42256030x 1 60 40 1 20 1 00 0 80 0 60 0 40 39 5042955231428 59 5042955231428 79 5042955231428 Concentration mg ml Absorbance A 1cm equivalent Curve fitting type Linear Display of result measured against the standard curve Full Scan e Use this mode to obtain a spectrum of a sample over the full wavelength range of the instrument 220 850nm to examine and compare spectra and to normalise one wavelength relative to another background correction e Select the Full Scan mode from the dialogue box e Pipette 2 5j l of Blank solution into a tip and place the tip and pipette adapter into the pipette holder see Correct pipette use and sample handling Click the button marked Blank Th
14. Tip 0 092cm 09 01 2013 13 32 Sample name 0 79 mg mL 11 81 pM Pipette Tip 0 092cm 0970172013 13 32 Sample name 0 10 mg mL 1 48 uM Pipette Tip 0 092cm 09 01 2013 13 33 Sample name 0 02 mg mL 0 00 uM Pipette Tip 0 092cm 09 01 2013 13 34 Sample name 0 40 mg mL 0 00 uM Pipette Tip 0 092cm 09 01 2013 13 35 Sample name 0 44 mg mL 0 00 uM 0 28 mg mL 0 00 j M Pipette Tip 0 092cm Delete Export Print Clear Overlays Example of results from Direct Protein measurement Export of data to Excel Data can be easily exported to Excel for subsequent analysis and normalisation for inclusion in reports etc To do this Double click on the results of interest Select the required data interval from 1nm or 0 1nm 1nm should normally be sufficient otherwise the data files will be extremely large Select the display format for data from Horizontal or Vertical Vertical is usually more manageable 09 01 2013 13 35 09 01 2013 13 49 Select the folder to which the data is to be saved and enter a file name Open Excel and navigate to the file in question note that data is exported as a text file LDpen the file it is a text delimited file with tab separation Manipulate that data as appropriate and save in the required format Picodrop CUBE User Manual version 1 0 May 2013 Page 20 Indirect Protein Me
15. applications where larger sample volumes are available a number of optional sampling devices can be used with this spectrophotometer Picodrop CUBE User Manual version 1 0 May 2013 Page 10 User and Data Management For full traceability all results are stored with the date and time of measurement along with an incrementing number This can be further enhanced by an alpha numeric name that can also be appended to every sample When making measurements results can be viewed in real time or exported in a tab delimited Microsoft Excel format for archiving or presentation in other programmes All spectrum scans have deep levels of zoom available in both the x and y axis ensuring the required level of detail can be viewed Graphical printouts can be made on low cost PC printers and include the scan results settings and sample information giving a concise hard copy record when required Picodrop CUBE User Manual version 1 0 May 2013 Page 11 INSTALLATION Unpacking Remove the instrument from the packaging and ensure the following items are included CUBE Spectrophotometer Unit Pipette Pipette Holder and Base Pipette Guide Collar Box of 96 UV pipette tips Ethernet Cable Fibre Optic Cables with Connectors 2 Mains cable with Plug o N DOU A WU N gt 9 12V Power Supply universal input voltage 10 1 5mm Allen Key for maintenance 11 Lens Extractor Tool for maintenance 12 Software Disk Any sh
16. ason for loss of power at the socket e Check the jack plug is securely connected to the rear panel connector If the power indicator still does not light check that 12V DC is available on the jack plug using a digital voltmeter take care not to short circuit the outer and inner contacts of the jack plug The centre contact should be 12V with respect to the outer If this voltage cannot be measured contact the manufacturer or your local distributor for support Picodrop CUBE User Manual version 1 0 May 2013 Page 28 Inconsistent result e Switch the instrument on and leave it for 10 minutes to come to thermal equilibrium e If you should obtain an unexpected erroneous result you should remove the pipette from the holder and immediately inspect the tip to check that sufficient sample remains in the tip The liquid column should be at least 2mm in height and should be continuous from the end of the tip i e no air gap at the bottom Leakage from the tip can occur if the tip is not securely attached to the pipette or if the end of the pipette tip is touched against the side of the pipette holder when placing the tip in the location hole Faulty and poorly maintained pipettes may also not retain the sample and should be verified by the following procedure e Re sample and check the liquid column in the tip both before and after sampling View the tip in the vertical position over a few minutes and check that there is no change in the liquid c
17. asurement General application information and background is described in the Appendix e Select the Indirect Protein mode from within the dialogue box e From the next dialogue box use Create to start a new method or Select to use a previously stored method 08 01 2013 16 44 08 01 2013 16 44 e If anew method is being created choose Bradford or Lowry if one of these standard techniques is to be used enter a suitable name for the experiment If not a new method is easy to set up by entering a suitable name the measurement wavelength and a background normalisation wavelength note that this must be entered Name Unit A Unit B Measurement A Normalization A e Press Proceed to go the define standards dialogue box Picodrop CUBE User Manual version 1 0 May 2013 Page 21 Pis Formula Fit 1 Finish e Pipette 2 5j l of Blank buffer solution into a tip and place the tip and pipette adapter into the pipette holder see Correct pipette use and sample handling e Click the button marked Blank The software will attempt to blank the spectrophotometer and set the baseline to zero the buzzing noise is due to the xenon lamp e If for any reason including air bubbles or settling turbidity in the sample a blank cannot be completed successfully a message requesting that you re blank will be displayed If this Occurs simply try blanking again and if the procedure cont
18. be achieved under normal conditions in a laboratory environment Our products are subject to continuous review and may be changed or up dated without notice Picodrop CUBE User Manual version 1 0 May 2013 Page 33 APPENDIX 1 APPLICATIONS Measuring Nucleic Acid Concentration and Purity The concentration of a sample can be calculated from its measured absorbance at its wavelength max All nucleic acids have a max at 260nm in the UV region of the electromagnetic spectrum The natural bandwidth of this peak is around 47nm so in line with good practice a spectrophotometer with a spectral bandwidth at least ten times less around 4nm must be used for measuring these samples From the Beer Lambert law A ecl where A is the absorbance is the molar extinction coefficient c the concentration and is the path length Where a 1cm path length cuvette is used solving the equation for concentration gives c AI In practice the measured absorbance is multiplied by a factor that is the reciprocal of the molar extinction coefficient as defined in the following table Nucleic Acid Molar Ext Factor 1 2 Resulting Units ssDNA 30 g 1cm 11 RNA 25 g 1cm 11 Oligonucleotid 33 g 1cm 11 ug ml or ng pl ug ml or ng pl ug ml or ng pl NOTE Where the nucleic acid has been diluted correction for the dilution ratio must be included All measurements are made at 250C and at a neu
19. d cat SAL2 mine Internet This computer E mine Private network Customize Access Local and Internet Connection Wireless Network Connection mine View status ui Signal strength Excellent Disconnect E Sharing and Discovery Network discovery File sharing Public folder sharing Printer sharing Password protected sharing Media sharing On On On read only password required off On On MH HM M M KO Show me all the files and folders I am sharing Show me all the shared network folders on this computer e Bik Double click on the wired Ethernet connection shown in the Local Area Connection Picodrop CUBE User Manual version 1 0 May 2013 Page 38 Ez Network Connections ll x Bluetooth Network Local Area Connection Wireless Network Connection a Network cable unplugged _ Connection x 6 dot connected e Bronja Netrane Giga alll mine You will then usually be asked to confirm a restricted system action by the Windows UAC User Access Control then Select Continue to allow configuration of the network adapter NOTE It may be necessary to disable other networks if there is an IP address conflict this can easily be done in the screen above by right clicking on each network in turn and selecting the Disable option Any disabled network can be switched back on by carrying out the same procedure and selecting the Enable option
20. e Do not use tools to tighten the knurled ring The completed assembly Always use the instrument with the pipette holder facing toward you and without excessive twisting of the fibre optic cables Note that the fibre optic cables on this instrument have a core of 100 j m so the bend radius is 4cm Picodrop CUBE User Manual version 1 0 May 2013 Page 14 Connection and loading the software to your PC The instrument has an external switch mode power supply that will accept any mains voltage from 100 to 240V AC at 47 to 63Hz If the correct mains plug has not been supplied an alternative lead or plug may be fitted If in doubt consult a qualified electrician Use only the power supply module supplied other makes although similar may damage the unit or cause erratic performance Connect the jack plug from the power supply module to the jack socket on the rear of the product Then switch the instrument on The LED on the front of the unit should be illuminated If it does not check all connections are made correctly and that the supply is switched on at the mains switch see also the Troubleshooting section Connect the instrument to a suitable PC using the short Ethernet cable supplied Note e The instrument should be connected directly to the Ethernet port other configurations are not supported e Itis important to set up your wired Ethernet connection as follows IP address 10 0 0 10 Subnet mask 255 0 0 0 The pr
21. e software will blank the spectrophotometer and set the baseline to zero at normalization wavelength if set the buzzing noise is due to the xenon lamp If for any reason including air bubbles or settling turbidity in the sample a blank cannot be completed successfully a message requesting that you re blank will be displayed If this occurs simply try blanking again and if the procedure continues to fail try following the lens cleaning protocol detailed in the Trouble Shooting Section Once the instrument has been successfully Blanked then the red Measure button will change to green signifying that you can commence measuring your samples Insert the pipette with sample and press the Measure button Click in the cursor box to enter a particular wavelength for which an absorbance value is required Picodrop CUBE User Manual version 1 0 May 2013 Page 24 2 00 1 60 1 20 0 80 Absorbance Al 1cm equivalent 0 40 0 00 220 270 Cursor Normalisation 220 0 1220 0 al 320 370 ID Mode 000259 Full Scan Full Scan Full Scan Full Scan Name Sample name Sample name Sample name Sample name Cursor absorbance Enable Notes 4 420 470 520 570 620 Wavelength nm Cursor 0 59 260 0nm 0 58 220 0nm 0 68 350 0nm 1 18 350 0nm Blank Path 10mm Cuvette 1cm 10m
22. e tip It is preferable that the sample tip and pipette holder are allowed to equilibrate to room e temperature before commencing measurement WARNING DO NOT LEAVE THE PIPETTE IN THE HOLDER FOR EXTENDED PERIODS AFTER MEASUREMENT HAS BEEN MADE Recommended pipetting procedure Picodrop CUBE User Manual version 1 0 May 2013 Page 17 Nucleic Acid Measurement e General application information and background is described in the Appendix e Select the relevant nucleic acid mode dsDNA ssDNA RNA from the dialogue box e Pipette 2 5yl of Blank solution into a tip and place the tip and pipette adapter e into the pipette holder see Correct pipette use and sample handling e Click the button marked Blank The software will run a reference scan on the spectrophotometer and set the baseline to zero For several seconds the LED on e the front of the unit will turn orange the buzzing noise is due to the xenon lamp e If for any reason including air bubbles or settling turbidity in the sample a blank cannot be completed successfully a message requesting that you re blank will be displayed If this occurs simply try blanking again and if the procedure continues to fail try following the lens cleaning protocol detailed in the Trouble Shooting Section e Once the instrument has been successfully Blanked then the red Measure button e will change to green signifying that you can commence measuring your samples
23. e tip avoid submerging the tip too far below the sample meniscus If necessary wipe off e excess liquid from outside of tip with a dry lint free tissue this is particularly e important if using viscous protein solutions Be careful not to touch the bottom of the tip as the sample may be drawn out by the tissue e The detection point in the tip is 2 5mm from the end so it is best procedure to try e not to submerge the tip more than 2mm into your solutions otherwise tip wiping may be necessary e Deeper insertion can leave residue on the tip and affect results e Use the same tip for blank and first sample this is similar to use of a conventional single beam spectrophotometer where the same cuvette is usually used unless an e optically matched pair available e Always place the pipette in the same relative position orientation in the holder have the pipette button or volume display facing out directly above the slot which is present in the holder Do not drop the pipette down into the holder take care when placing it into the holder e Do not place the UV pipette tips or your sample too close to heaters or the fan of the e PC as heating the tips or sample may result in a rapid contraction in volume once the tip is placed in the cooler pipette holder This sample contraction will result in a e space or bubble being visible at the bottom of the tip This space may interfere with sample measurement if allowed to rise more than 2mm up th
24. ent and reagents that may be required for this as well as to the proximity of a suitable and safe waste disposal system The instrument should be positioned within 2 0 meters of an easily accessible mains socket preferably with an isolating switch The Ethernet cable supplied is 1 metre long so the PC will need to be positioned so the Ethernet port can be reached by this cable Picodrop CUBE User Manual version 1 0 May 2013 Page 12 Please ensure that the ventilation slots of the device remain clear and free to vent at all times A space of at least 10cm should be left around the spectrophotometer The space underneath the instrument must be kept clear of paper loose material and dust build up The ambient temperature should be between 10 C and 30 C the humidity between 0 and 95 non condensing Hardware installation if not already pre assembled Assembling the pipette holder The pipette holder has been dismantled and disconnected for shipment Fix the tubular pipette holder to its round base by simply screwing it on Connecting the fibre optic cables Important 1 Although they carry out a similar interconnection function to electrical cables fibre optic cables are made of glass and CANNOT be handled in a similar manner to metal based conductors 2 Do not exceed the maximum bend radius for the cable in use or in storage This is typically 300 times the cladding diameter so for core diameters of 100m to 600pm this approxima
25. ew connection Set up a home or small office network Change Windows Firewall settings Disable this network device Eat Rename this connection L Change settings of this JiFi Link 5300 AGN Wireless Network Connection 1394 Connection C d ec Conn d ga 1394 Net Adapter NOTE It may be necessary to disable other networks if there is an IP address conflict this can easily be done in this screen by right clicking on each network in turn and selecting the Disable option Any disabled network can be switched back on by carrying out the same procedure and selecting the Enable option Select Internet Protocol TCP IP from the following screen ensuring that the checkbox to the left of the item remains checked Now click on Properties Local Area Connection Properties Ej Realtek RTL8168D P 8111D P PCI This connection uses the following items Bert for Microsoft Networks A File and Printer Sharing for Microsoft Networks Z QoS Packet Scheduler Intemet Protocol TCP IP Description SS lt j l lt ra Select the radio button next to Use the following IP address Enter the values as shown to the image to the right and click OK to save changes Make sure that there are no other network adapters active you may need to consult your system s user manual to achieve this Picodrop CUBE User Manual version 1 0
26. h fibre optic coupled sampling accessories Because there are NO MOVING PARTS the inherent reliability and durability of these instruments far surpasses those of traditional design calibration is fixed in manufacture so no delays are needed at switch on for a lengthy auto cal procedure while maintenance and service requirements are truly minimal The product uses a press to read system with a pulsed xenon lamp that is only powered up when a measurement is being made This not only saves energy compared to spectrophotometers with lamps that are continuously on but gives a much longer lamp life in excess of 10 years with far higher UV energy levels Light from the xenon lamp is transmitted to the sampling accessory via a fibre optic cable Here some wavelengths are absorbed by the sample while the light transmitted through it is then returned to the polychromator and CCD Array detector by another fibre optic cable on the other side of the accessory This enables the sampling accessory to be remote from the instrument and for dedicated application specific sampling accessories to be designed without Fibre OpticCable the restrictions of the traditional light tight sample to polyehromator chamber being required This also simplifies and OE speeds up operation as there is now no need to keep EE opening and closing sample chamber lids for each measurement Fibre Optic Cable from Light Source Dedicated Sampling Accessory P
27. he spectrophotometer and set the baseline to zero the buzzing noise is due to the xenon lamp If for any reason including air bubbles or settling turbidity in the sample a blank cannot be completed successfully a message requesting that you re blank will be displayed If this occurs simply try blanking again and if the procedure continues to fail try following the lens cleaning protocol Picodrop CUBE User Manual version 1 0 May 2013 Page 19 e Once the instrument has been successfully Blanked then the red Measure button will change to green signifying that you can commence measuring your samples o Insert the pipette with sample and press the Measure button e Note When using viscous samples it is important to ensure that the sample does not adhere to the outside of the tip Simply wiping the outside of the tip with a piece of clean dry tissue will normally avoid this potential problem o After afew seconds the concentration in mg ml will appear in the bottom right hand window the spectrum will be plotted and details displayed in the table below the graph It is not necessary to save the results as all results are done so automatically Absorbance A 1cm equivale eee ee Wavelength nm Result Path Date Time Sample name 1 54 mg mL 23 14 uM Pipette Tip 0 092cm 09 01 2013 13 32 Sample name 1 52mg mL 22 84 uM Pipette
28. icodrop CUBE User Manual version 1 0 May 2013 Page 8 This configuration also isolates the lamp from the sensitive optics of the polychromator so problems of heat and stray light from the light source become a thing of the past The polychromator in the instrument is effectively a sealed unit with a single fibre optic cable as input and a single ribbon cable as output Compare this to traditional spectrophotometers where the lamp is usually an integral part of the monochromator requiring forced cooling and so introducing dust and contamination into the optics increasing maintenance degrading performance and shortening its working life As well as removing all moving parts another major advantage of the polychromator used in the product over the monochromator used in traditional spectrophotometers is the speed of measurement with a full scan being possible in around 2 seconds while the 3648 element CCD Array ensures a fine resolution of the detail Measurement Modes This instrument has modes for measuring Nucleic Acids as both double stranded DNA dsDNA and single stranded DNA ssDNA as well as RNA The concentration and purity ratio of the nucleic acid are reported along with a full wavelength scan all ina measurement time of 2 seconds Direct Protein measurements can be made against a general Absorbance reference as well as BSA IgG Lysozyme or user entered reference Indirect Protein measurements can be made using the Bradford
29. igate to the file in question note that data is exported as a text file e Open the file it is a text delimited file with tab separation e Manipulate that data as appropriate and save in the required format Direct Protein Measurement General application information and background is described in the Appendix e Select the Direct Proteins mode from the dialogue box Lysozyme Other The options listed are detailed below e A280 setting based on a 0 1 1 mg ml protein solution producing an Absorbance at 280 nm of 1 0 A where the path length is 10 mm e BSA Bovine Serum Albumin unknown sample protein concentrations are calculated using the mass extinction coefficient of 6 7 at 280 nm for a 1 10 mg ml BSA solution e Jop unknown sample protein concentrations are calculated using the mass extinction coefficient of 13 7 at 280 nm for a 1 10 mg ml IgG solution e Lysozyme unknown sample protein concentrations are calculated using the mass extinction coefficient of 26 4 at 280 nm for a 1 10 mg ml Lysozyme solution e Other user defined mass extinction coefficient L gm 1cm 1 for a 10 mg ml 1 solution of the respective reference protein o Pipette 2 5j l of Blank buffer solution into a tip and place the tip and pipette adapter into the pipette holder see correct pipette use and sample handling o Click the button marked Blank The software will attempt to blank t
30. inues to fail try following the lens cleaning protocol detailed in the Trouble Shooting Section e Once the instrument has been successfully Blanked then the red Measure button will change to green signifying that you can commence measuring your standards and replicates e To begin recording the concentrations of your known standards 0 Choose Add to get the Measure standards dialogue box Enter the known concentration of your standard place the pipette tip containing your standard into the instrument 0 Press Replicate 1 to measure the absorbance of the standard Up to 5 replicates of the same standard can be measured and the average value displayed 0 Press Done when the replicates for this standard are complete Picodrop CUBE User Manual version 1 0 May 2013 Page 22 foo a Replicate 1 Replicate Replicate Replicate Replicate Average absorbance Concentration Repeat this step for each standard until the standard curve is complete e Select the curve fit required linear regression quadratic and cubic quartic e Note that a minimum of 2 standards are necessary to draw a linear regression standard line curve R 0 998663194125419 Formula Y 7 05023256 66 42256030x 1 60 1 40 1 20 1 00 0 80 0 60 Absorbance A 1cm equivalent 0 40 39 5042955231428 59 5042955231428 79 5042955231428 99 5042955231428 Concentration mg ml Curve fitting type
31. les at their exit point from probe heads in use and storage and do not support the weight of a probe by the cable 10 Do not use any cable cable assembly or probe beyond its specified performance limits or outside of its environmental operating and storage conditions If in doubt consult your supplier alternatives may be available specials suitable for most situations can often be supplied or alternative procedures developed Procedure Fitting the two fibre optic cables to the instrument Connect the SMA to SMA launch cable from the lamp socket top right by pushing the connector into the socket and hand tighten the knurled ring completely to hold the connector in place Do not use tools to tighten the knurled ring No polarity or orientation needs to be observed Connect the MTP to SMA collection cable to the detector bottom left by pushing into the slot note that to remove it the shroud should be pulled back Fitting the fibre optic cable to the pipette holder Ensure that the launch cable from the lamp socket is connected to the pipette holder with the holder slot facing forward and on the right hand side of the holder Ensure that the collection cable to the detector is connected to the pipette holder with the holder slot facing forward and on the left hand side of the holder see diagram In both cases push the connector into the socket and hand tighten the knurled ring completely to hold the connector in plac
32. m Cuvette 1cm 10mm Cuvette 1cm 10mm Cuvette 1cm Delete Export Print Clear Overlays 670 720 Normalisation A none An example of a full wavelength scan potassium dichromate solution Zoom al 770 820 Date Time 09 01 2013 16 01 09 01 2013 16 02 09 01 2013 16 07 09 01 2013 16 10 Measure To zoom in to an area of interest move the pointer to a position on the graph then click the left mouse button and hold down whilst moving the pointer to another position A rectangle will be drawn Releasing the left mouse button will activate the zoom magnification To reset the zoom back to normal click on Reset Zoom as shown at the bottom of the graph window Graph overlay It is possible to superimpose graphs for up to 7 samples onto the same graph window by simply clicking on the sample displayed in the table under the graph Overlays can be removed by clicking on Clear overlays shown at the bottom of the graph window Picodrop CUBE User Manual version 1 0 May 2013 Page 25 Absorbance A 1cm equivalent 3 303 645820669244 353 645820669244 403 645820669244 453 645820669244 alia Cursor A Cursor absorbance 220 0 ID Mode Name _ Cursor Path Normalisation J Date Time Full Scan Sample name 1 00 230 Dm 10mm Cuvette 1cm none 09 01 2013 15 24 Full Scan Sample name 1 14 220 0nm 10mm Cuvette 1cm 09 01 2013 15 24
33. n using 1cm pathlength cuvettes gives c A e then A emolar molar concentration However many sources do not provide molar extinction coefficients Instead they provide absorbance A280nm values for 1 solutions which are 1 g 100 ml measured in a1 cm cuvette These values can be understood as percent extinction coefficients epercent with units of g 100 ml 1 cm 1 instead of M 1cm 1 Consequently when these values are applied as extinction coefficients in the general formula the units for concentration c are percent i e 1 1 g 100 ml 10 mg ml A percent percent concentration To report concentration in terms of mg ml then an adjustment factor of 10 must be made when using these percent extinction coefficients i e convert from 10 mg ml to 1 mg ml A percent 10 concentration in mg ml The relationship between molar extinction coefficient emolar and percent extinction coefficient epercent is as follows emolar 10 percent x molecular weight of protein Still other sources provide protein absorbance values for 0 1 mg ml solutions as this unit of measure is more convenient and common for protein work than percent solution This variation in reporting style underscores the importance of carefully reading stated values to be sure that the unit of measure is understood and applied correctly Picodrop CUBE User Manual version 1 0 May 2013 Page 36 Measuring a Protein or Protein Mixtu
34. observed e Before returning any item for service repair or calibration a Decontamination and Safety Clearance Declaration must be completed to ensure the duty of care can be maintained for those who will be handling equipment used for such purposes Solvent Compatibility Instrument case and paintwork Compatible Solvents Acetic Acid dilute Chloroform Methanol Acetone Ethanol N Propane Acetonitrile Ether Sodium Hydroxide Benzene HCI dilute Sodium Hypochlorite Bleach Hexane Toluene Butanol HNO3 dilute Carbon Tetrachloride Isopropanol Incompatible Solvents Hydrofluoric Acid and derivatives Picodrop CUBE User Manual version 1 0 May 2013 Page 7 INTRODUCTION General This instrument is a low volume short path length spectrophotometer that provides the user with the facility to recover their sample after measurements have been taken using in tip UV pipette technology It is a full spectrum 220 850nm UV Visible spectrophotometer which allows for measurements of many sample types commonly analysed in the laboratory Because of its ultra small sample requirement and ability to recover the samples the product is ideally suited to life science applications including DNA RNA and protein measurements and includes a sampling accessory and software dedicated to these applications Principle of Operation This instrument is one of a new type of spectrophotometer that integrates a high resolution CCD Array detector wit
35. ocedure for setting IP addresses is covered in the appendices at the end of this manual for Windows Vista Windows XP Windows 7 and Windows 8 Please go to this section now To install the software insert the CD ROM supplied in the CD Drive of the computer The disc should Auto run if not go to Windows Explorer right click on the disc and select Auto play Minimum specification for the PC Microsoft Windows XP Service Pack 2 Vista or Windows 7 512Mb RAM 2 8GHz Pentium 4 or 1 6GHz Core Solo or Core Duo A Microsoft DirectX 9 compatible graphics card with at least 64Mb of on board RAM e g Nvidia GeForce 5900 or better 200Mb of free disc space One Ethernet port Please click on the Setup file The software will install automatically leaving a shortcut on the desktop to the instrument interface If the installation has been completed successfully after double clicking the desktop icon the initial screen will be displayed and it will be possible to login as a guest and select the New file option Picodrop CUBE User Manual version 1 0 May 2013 Page 15 APPLICATION MODES Getting Started e Once the software has installed correctly an icon will be visible on the desktop and there will be option from the Start button Select CUBE and the following dialogue box will appear Nucleic Acids Direct Proteins Full scan licroarra Indirect Proteins e Before using the instrument for the first
36. olumn in the tip and specifically that there is no formation of a meniscus outside the end of the tip as this indicates that the seal between tip and pipette or in the pipette itself is damaged e If this test proves satisfactory and the result is still not good increase the sample volume to say 3pl and do the visual checks before and after measurement e H having completed this results are still not satisfactory follow the Quick Clean procedure detailed on the previous page e Ifthe results are still not good then the following lens cleaning procedure should be adopted as detailed on the following page Picodrop CUBE User Manual version 1 0 May 2013 Page 29 Lens cleaning procedure Please note that as the lenses get dirty with use then the stability will decrease and this will accentuate any background noise and small variations between tips e Detach the optical fibres by unscrewing from each side of the pipette holder e Use the 1 5mm Allen key as supplied to loosen the 2 fibres by turning the two sunken screws in the front of the bottom of part of the pipette holder and then pull gently the two fibres away from the holder ONLY pull on screw head closest to holder do not pull directly on the fibre cable The lenses are fixed to the ends of each fibre Important if the fibres do not come away from the holder easily please seek assistance from the manufacturer of your Distributor e Check whether either lens at
37. operties Description Transmission Control Protocol lntemet Protocol The default wide area network protocol that provides communication across diverse interconnected networks You can get IP settings assigned automatically if your network supports this capability Otherwise you need to ask your network administrator for the appropriate IP settings Obtain an IP address automatically Use the following IP address IP address Subnet mask Default gateway Obtain DNS server address automatically Use the following DNS server addresses Preferred DNS server Alternate DNS server E Validate settings upon exit TF Select the radio button next to Use the following IP address and enter values shown in the image above and click OK to save changes Make sure that there are no other network adapters active you may need to consult your system s user manual to achieve this Picodrop CUBE User Manual version 1 0 May 2013 Page 43
38. or Lowry protocols as well as against user defined settings Full wavelength scan is also available with zoom and overlay facilities A wavelength may be selected for normalization or background correction More information on applications is provided in the Appendix Principle of Measurement Micro sample accessory Using a novel through the tip measurement principle samples as small as 2 5ul can be measured and still be retained for further processing or other analysis Using the specially designed micro sampling accessory samples remain protected and contained within the special UV transmitting pipette tips where they are measured They do not have to be dispensed so there is no risk of the cross contamination or carry over that can occur with methods that require dispensing the sample onto a platform or pedestal There are no caps or covers to be placed over the sample so measurement is quick and easy Precious samples can be handled within a sterile environment and are completely recoverable Using individual disposable tips for each sample means there is no need to clean up after each measurement removing any possibility of carry over or contamination and making this the fastest and most efficient method of analysis Picodrop CUBE User Manual version 1 0 May 2013 Page 9 A 2 5pl sample is drawn up directly into the UV pipette tip using the supplied pipette The pipette is placed into the holder which automatically positions the
39. ortages or damage must be reported to the carrier and your local distributor as soon as possible Keep all packaging materials in case the unit has to be re shipped or stored at a later date always place items in clean polythene bags before packing to avoid the ingress of fibres and dust from the cardboard Positioning The ideal installation environment for the instrument and its accessories will be clean dry and dust free with the temperature and humidity controlled All items should be sited away from windows where extreme and rapidly changing temperatures can be experienced even in a controlled environment The spectrophotometer should be placed on a rigid flat clean surface Make sure that the instrument is completely stable Where the ideal conditions cannot be met the instrument and its accessories must be given additional protection both when in use and idle Protection suing dust covers is always recommended when equipment is not in use Where conditions are less than ideal routine maintenance and cleaning may be required more frequently The instrument requires a bench area of just 30 x 16 cm and the micro sample accessory just 78 square centimeters Further consideration should be given to the space for and location of the PC required to drive the product as well as other peripheral devices such as printers etc When choosing a location thought should also be given to the additional space required for sample preparation and the equipm
40. rch programs and files P Seen gt 16 43kb JPEG From the control panel screen select the Network and Internet option as shown below ensure that View by Category is selected Dap P JONE Control Panel Adjust your computer s settings or search for specific tasks System and Maintenance Get started with Windows User Accounts and Family Safety Set up parental controls for any user 4 A Back up your computer Security Check for updates Check this computer s security status Allow a program through Windows Firewall Network and Internet Connect to the Internet View network status and tasks Change HomeGroup and sharing settings Hardware and Sound Play CDs or other media automatically Printer Mouse Programs Uninstall a program Change startup programs as Gore Add or remove user accounts Appearance and Personalization Change desktop background Customize colors Clock Language and Region Change keyboards or other input methods Change display language Ease of Access Let Windows suggest settings Optimize visual display All Control Panel Items From the Network and Sharing Centre on the next screen select Change Adapter Settings in the upper left corner of the screen Picodrop CUBE User Manual version 1 0 May 2013 Page 42 e ku S Hi Network and Internet Network and Sharing Center Control Panel Home Change adap
41. re compliant with the following standards LAV Directive 72 23 EC LEMC Directive 89 336 EC Note This declaration of conformity becomes invalid if The devices are installed modified complemented or changed in a manner which has not been permitted in the devices User Manual In case of improper usage Picodrop Ltd Picodrop CUBE User Manual version 1 0 May 2013 Page 5 ESSENTIAL SAFETY NOTES All product and brand names used in this document are trademarks or registered trademarks of their respective holders Please read carefully before installing or operating this instrument if in doubt seek advice 1 This instrument is designed for operation by trained personnel who are aware of the principles and applications involved For further help and advice please contact your distributor or visit www Picodropsytems com 2 This instrument is a sensitive optical and electronic instrument designed for use in a laboratory environment Careful adherence to the installation instructions must be observed If in doubt contact a relevant and competent authority before proceeding 3 Operators of this instrument must be trained in a general laboratory safety practices b the specific safety requirements of the instrument and any other equipment being used and c the risks and safe practices for the analysis being undertaken including those associated with sample handling If the equipment is used in a manner not specified b
42. re with Unknown Extinction Coefficients Most published protein extinction coefficients range from 4 0 to 24 0 epercent however the distribution is skewed in favour of the lower values giving a mode of 10 If no extinction coefficient information exists for a protein or protein mixture of interest and a rough estimate of protein concentration is required for a solution that has no other interfering substances common practice is to assume an percent value of 10 Therefore although any given protein can vary significantly from this approximation the average for a mixture of many different proteins will most likely be approximately 10 Note the software assumes the user has entered the percent value as defined above The software converts Absorbance at 280nm into mg ml of protein using the follow Formula Protein Conc in mg ml A280nm corrected to 10mm path length epercent x 10 Picodrop CUBE User Manual version 1 0 May 2013 Page 37 APPENDIX 2 SETTING IP ADDRESSES Setting IP addresses in a Windows Vista system Open the Control Panel by pressing the Start button and then selecting Control Panel Ell OO E control Panel a a Ele Edit View Tools Help Control Panel Home Classic View Name CH KX Add Hardware Administrative Adobe Gamma Tools E Ease of Access Center Folder Options Fonts Z s Backup and BitLocker Drive Restore Encryption AutoPlay D 3
43. respectively The choice of which method to use will depend on the expected range of the samples solvent and extraction reagent compatibility preparation time restrictions and the ease of use required Please refer to your reagent kit supplier and the pack insert for full details of limitations and restrictions sample preparation procedures and respective analytical performance Indirect methods have been developed to ensure all proteins in a mixed sample are measured correctly Direct measurement The direct method requires little or no sample pre treatment so has a lower cost and is much quicker and easier to perform than the indirect methods but is less accurate when measuring mixtures of proteins Although all proteins have a max at 280nm their molar extinction coefficients vary so the correct n factor or extinction coefficient has to be chosen for different sample types to ensure they are measured accurately The following table gives details of these extinction coefficients Concentration at 1 0 mg ml 9 o rea TT _ A T J Ta TT TT 8 Tawan TT 2 omer tere Picodrop CUBE User Manual version 1 0 May 2013 Page 35 Molar Extinction Coefficients vs Absorbances for 1 Solutions Using the molar extinction coefficient in the calculation of protein concentration gives a result in terms of molarity We know from the Beer Lambert law that absorbance A bc and solving this equation for concentratio
44. ser They can be cleaned using water or a mild laboratory cleaning agent e g ethanol or general lab cleaner The instrument should not come into contact with aggressive solutions Ensure that no liquid enters the spectrophotometers For safety reasons the device must be switched off and disconnected from the power supply prior to cleaning Quick Clean procedure for sample holder In the event that sample leaks from a pipette tip or dust reduces the light transfer through the pipette holder simply unscrew the fibre optic cables from each side of the pipette holder no tools required silver screws should be only hand tight Unscrew the circular base from the tube section Either soak the holder in hot water with detergent for 30mins and air or drip dry or alternatively simply wash with ethanol or a similar solvent Reassemble and re test instrument If this quick clean procedure does not improve the results please follow the Service Clean procedure described below Troubleshooting Power indicator does not light e Check that the external power supply unit is plugged into a mains outlet and that this is switched on if an extension socket is being used trace this back to the original wall socket and ensure this is switched on and working Check power is available at each socket by substituting a known working device and ensure this is OK If power is still not available contact a trained and qualified electrician to identify the re
45. t condition must be reported to the appropriate servicing authority as soon as possible In all such reports the model name number and serial number must be quoted Picodrop CUBE User Manual version 1 0 May 2013 Page 6 Potential Safety Hazards Electrical Standard electrical safety precautions should be observed e Ensure that the proper voltage is being supplied before turning the instrument on for the first time e The device must be connected to a grounded socket e Do not touch any switches or outlets with wet hands e Switch the instrument off at the mains supply before disconnecting the AC power cord e Unplug the instrument prior to maintenance cleaning up any major liquid spills and prior to servicing any of the electrical or internal components e Ifin doubt about any aspect of the electrical installation consult a qualified electrician Only qualified personnel should perform electrical servicing Hazardous Substances e Reference should always be made to the health and safety data for any chemicals or reagents used All advice and warnings on the handling storage use and disposal of these must be carefully observed When not available this data must be requested from the supplier before proceeding in any way e The relevant safety regulations must be observed when handling pathogenic samples radioactive materials or other substances hazardous to health The correct and safe disposal of waste materials must be
46. ter settings A Change advanced sharing settings MCLAUGHLIN7 X64 This computer View your active networks Network Work network Change your networking settings access point Sr Connect to a network See also HomeGroup Troubleshoot problems Internet Options Windows Firewall Double click on Local Area Connection View your basic network information and set up connections FH See full map Internet Connect or disconnect Access type Internet Connections Local Area Connection K Set up a new connection or network Set up a wireless broadband dial up ad hoc or VPN connection or set up a router or Connect or reconnect to a wireless wired dial up or VPN network connection ef Choose homegroup and sharing options Access files and printers located on other network computers or change sharing settings Diagnose and repair network problems or get troubleshooting information Highlight Internet Protocol version 4 and ensure it remains ticked Then select the Properties button Networking Connect using i Network Connection This connection uses the following items OM Client for Microsoft Networks Bas Packet Scheduler B File and Printer Sharing for Microsoft Networks 4 Intemet Protocol Version E TCP IPv6 intemet Protoco 4 TCP IF Link Layer Topology Discovery Mapper 1 0 Driver Link Layer Topology Discovery Responder Install L Uninstall Pr
47. tes to a bend radius of 4cm 100ym to 20cm 600um but is dependent on the detail of the construction of each cable type The fibre optic cables on this instrument have a core of 100ym so the bend radius is 4cm 3 Ensure all optical surfaces are clean and dust free before making any connections Always replace dust caps on fibre ends and instrument SMA905 connectors when fibre optic cables are disconnected 4 Do not use tools to tighten the screw locking ring on SMA905 connectors but do ensure they are firmly hand tight 5 Do not pull on the cable to remove it when disconnecting only use the connector screw locking ring Picodrop CUBE User Manual version 1 0 May 2013 Page 13 6 Do not subject the cable to axial twisting in use installation or storage Spool or un spool long lengths of cable in a figure of eight as each part of the eight puts an opposite twisting moment in the cable turn the eight over when carrying out the reverse process 7 Do not subject the cable to pulling stress during installation or use Fibres are usually stronger in direct tension relative to the cross section but when fibres are small it is very easy to break them Unfortunately each cable construction will have its own limits and it is difficult to give fixed rules for this so minimizing pulling stress is important 8 Try to restrict movement of cables during the period a measurement is being made 9 Take extra care not to bend or crush cab
48. the end of each cable is wet This happens when excess sample is picked up on the outside of the tips e Wash each lens with pure water and dry with tissue e Use a cotton tip soaked in acetone to clean and dry the lenses e Remove the round base from the holder by unscrewing e Thoroughly rinse the metal base unit in pure water and then allow to air dry e Re assemble unit Picodrop CUBE User Manual version 1 0 May 2013 Page 30 Connection Lost message This message tells the user that the spectrometer has crashed Disconnecting the power from the spectrometer and reconnecting it should solve the problem There is no need to shut down or restart the software and your data should remain intact Communications Error message In the event of a software hang up or communications glitch a message will be displayed Click on Details to view the information there this should be copied pasted into an email and Ethernet Connection failed e To check the connection between instrument and the PC open a command prompt by pressing the Start button in the bottom left corner of the screen and then select All Programs and then select Accessories and then select Command Prompt once the Command Prompt window has appeared type ping 10 0 0 10 and then press return Command Prompt Microsoft Wind Version 6 1 7601 Copyright Ceci 2889 Microsoft Corporation All rights reserved C Users Astranet gt ping 10 0 0 123
49. tral to slightly alkaline pH The instrument automatically corrects for the reduced pathlength of the UV pipette tips The factor can also be determined from the slope of a linear calibration plot of absorbance versus concentration for the pure nucleic acid under consideration This also enables us to define a simple range of stock calibration and QC standards as Follows A solution of 50 ug ml or 50 ng l dsDNA will give a reading of 1 00A at 260nm A solution of 33 ug ml or 33 ng pl ssDNA will give a reading of 1 00A at 260nm A solution of 40 ug ml or 40 ng pl RNA will give a reading of 1 00A at 260nm The instrument compensates for samples where particles in suspension or background turbidity may be a problem by subtracting the absorbance at 320nm The Purity Ratio determines the level of contamination from proteins and is based on the absorbance of these at 280nm For pure DNA the 260 280 ratio should be 1 8 for RNA it should be 2 0 lower values indicate contamination by proteins Picodrop CUBE User Manual version 1 0 May 2013 Page 34 Protein Measurements Proteins can be measured directly at their max of 280nm or indirectly by adding reagents to the sample to produce a colour proportional to the protein concentration and then measuring at the wavelength of maximum absorbance max for that colour Indirect measurement This product is pre programmed with the Bradford and Lowry indirect methods where analysis is at 595nm and 750nm
50. ttings Obtain an IP address automatically Use the following IP address IP address Subnet mask Default gateway Obtain DNS server address automatically Use the following DNS server addresses Preferred DNS server Alternate DMS server E Validate settings upon exit Setting IP addresses in a Windows XP system Open the Control Panel by pressing the Start button and then selecting Control Panel Control Panel File Edit View Favorites Tools Help e Back 2 Search RE Folders E Si Folder Sync Address control Panel z a 2 2 wh G 2 amp Accessibility Add Hardware Add or Administrative Andrea Noise Automatic Date and Time Display Fol G Switch to Category View Options Remov Tools Cancellatio Updates Mail MobileMe Network Setup NVIDIA NVIDIA nView Phone and Pov Windows Update Help and Support Wg e E E lt Speech System Taskbar and User Accounts Windows Windows Wireless Start Menu CardSpace Firewall Network Set Now double click Network Connections then Local Area Connection Picodrop CUBE User Manual version 1 0 May 2013 Page 40 s Network Connections File Edit View Favorites Tools Advanced Help Back Q ba Us search E Folders E Sei Folder Sync Address S Network Connections LAN or High Speed Internet focal Area Connection Network cable unplugged d Realtek RTL8168D P 3111D T Bi Create a n
51. y and that any conflicting network settings have been disabled e Other Networks can be disabled by selecting the Networks option in the Control Panel clicking on one of the other networks to highlight it then by right clicking the highlighted network and selecting Disable carry out the same procedure with each unwanted network These can be re enabled by carrying out the same procedure and selecting the Enable option Picodrop CUBE User Manual version 1 0 May 2013 Page 32 SPECIFICATIONS Pathlength Pathlength using optional cuvette holder Sample volume _Microvolume samples tandard samples Light Source Detector Photometric Linearity Photometric Range Wavelength Range Wavelength Accuracy Spectral Bandwidth Absorbance Precision Detection Limit DNA Detection Limit BSA Read Time Communication Power Dimensions Weight Nominally 1mm or 10mm with optional cuvette 10mm 5mm 1mm or 0 5mm depending on the type of cell used 2 5ul from microplate well or Eppendorf tube up to 2ml volume Up to and over 2 5ml if cuvette holder or iPulsed Xi enon Lamp powered for reading only 3648 pixel CCD Array UV enhanced Better than 0 2 to 2 5A 220 to 850nm 0 5nm lt 2nm 0 003A 3ng ul 0 1mg ml 2 seconds includes full wavelength scan PC Ethernet cable supplied 24 DC from supplied adapter with input 100 18x18x17 cm 3 5kg These specifications reflect the performance that can
52. y the manufacturer the protection provided by the equipment may be impaired and any warranty invalidated 4 This instrument is designed for minimal maintenance which must be carried out carefully following the procedures detailed in this manual All safety instructions detailed in these procedures as well as those for the area or environment where the work is being carried out must be observed 5 Other than for those items defined in the maintenance procedures there are no user serviceable items in this instrument Removal of covers and attempted adjustment service or modification by unqualified personnel will invalidate any warranty and incur additional charges for repair 6 Reference should always be made to the health and safety data for any chemicals or reagents used All advice and warnings on the handling storage use and disposal of these must be carefully observed When not available this data must be requested from the supplier before proceeding 7 It is important that good laboratory practice is observed when handling samples chemicals reagents and ancillary equipment in order to carry out measurement and analysis with this instrument Suitable personal protective equipment PPE must be used at all times and in all circumstances 8 If it is suspected that safety protection has been impaired in any way the instrument must be made inoperative and be secured against any intended operation with clear warnings as to this state The faul

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