Agilent G3835AA MassHunter Profinder Software
Contents
1. i File Edit View Method Wizards H e When you click Add Remove New Project Sample Files after launching 3l Open Project Profinder Profinder starts a new Save Project project as if you clicked File gt New Save Project as Project Add Remove Sample Files Export as CEF Export as CSV Export as Detailed CSV 3 Add files to the Add Sample Files Click Add file s to display the Open dialog box file dialog box Add Remove Sample Files Sample file selection and display order Show Hide Samples Polarity Sample Group Add filele oK Cancel 16 Profinder Quick Start Guide Basic Profinder Workflow Steps 4 Select at least one sample data file in the Open file dialog box Open file Detailed Instructions a Browse to the folder containing your sample files b Select at least one sample data file c Click Open Laak irt F Raia Files O Pl les 3 Reci ene My Documents Desktop Computer A Network 5 Optional Enter Sample Group value to the sample files in the Add Sample Files dialog box Eg d Eg Eg BE Eg P F ik P 1 1_Control_000 d B 1 2_Control_O00 d Bik i Control _000 d W 1 4_Control_000 d _Infected_000 d 2 2_Intected_O00 d 3_Infected_O00 d 4 Infected _OO0 d 1_Control 250 3 2 _Control_250 d 3 Control 250d 4 Control 250d P 4 1_Infected_250 d ihi d 2_Infected_i 250 d p 4 4 nfected_ 250 d Fi2. Agg Agilent Technologies
3. in the same application without moving CEF files back and forth between MassHunter Qualitative Analysis DA Reprocessor and Mass Profiler Professional as illustrated in Figure 1 on page 4 Batch Recursive Feature Extraction Method MFE MFE Compound MFE Post Fbl Matching Fbl EIC Peak Fbl Spectrum Fil Extraction Compound Binning and Processing Tolerances and Integration and Extraction and Post Processing Parameters Filters Alignment Filters Scoring Filtering Centroiding Filters Step 1 of 8 Step 2 of 8 Step 3 of 8 Step 4 of 8 Step 5 of 8 Step 6 of 8 Step 7 of 8 Step 6 of 8 Chromalogram Figure 7 Eight steps are presented in the Batch Recursive Feature Extraction Method wizard 26 Profinder Quick Start Guide Feature Extraction Workflow Algorithms Batch Targeted Feature Extraction Targeted feature extraction TFE uses an input formula source CEF file or database containing molecular formulas mass and or retention time information to extract features from your data using a process referred to as Find Compounds by Formula After feature extraction is performed compound alignment produces a result such that one compound target can only have one compound extracted per data file Find Compounds by Formula typically uses molecular formula information to calculate the ions and isotope patterns derived from the formula as the basis to find features in the sample data file When the input molecular feat
4. method 18 Profinder Quick Start Guide Basic Profinder Workflow Select your feature extraction algorithm and then edit and run the method Three feature extraction algorithms are available in Profinder Batch Molecular Feature Extraction MFE Batch Recursive Feature Extraction RFE default Batch Targeted Feature Extraction TFE An overview of each extraction algorithm is found in the section Feature Extraction Workflow Algorithms on page 25 Each algorithm is designed to efficiently extract the features compounds in your sample data files Steps Detailed Instructions 1 Select the feature extraction a Click one of the three algorithms algorithm to apply to your samples b Click Next Feature Extraction Workflow Select the feature extraction algorithm to run Batch Molecular Feature Extraction Batch Recursive Feature Extraction Batch Targeted Feature Extraction Next Finish Cancel 2 Review and edit the parameters for the feature extraction algorithm a Make changes to the parameters on each wizard tab for each step b Click Next to go to the next step of the wizard c Click Previous to return to an earlier step Help Previous Next Finish Cancel Profinder Quick Start Guide Comments e MFE performs chromatographic deconvolution and aligns the features across the selected sample files using mass and RT See Batch Molecular Feature Extraction on page 25 for the
5. wizard steps RFE performs MFE and then uses the mass and RT of each feature to perform a targeted feature extraction See Batch Recursive Feature Extraction on page 26 for the wizard steps TFE uses an input formula source CEF file or database to extract features See Batch Targeted Feature Extraction on page 27 for the wizard steps Click Help to activate online Help specific for the current tab in the wizard Click Cancel to stop editing the algorithm parameters Any changes made to the algorithm parameters are not saved 19 Basic Profinder Workflow Steps Detailed Instructions 3 Run the feature extraction a Click Finish to run the extraction algorithm algorithm on your sample data b An Operation in Progress dialog box is displayed while the extraction process is running Operation in Progress Data file 5 of 16 2 1_Infected_000 d a 35 Searching for positive ion mass features 4 Review your results e Review your results and then export the results and save your method E apimi misiuni Profereder 608 00 Tagar APT Profinder Mirt aicigami p m 20 Comments The feature extraction process can take a long time Example processing times for sixteen 16 LC MS data files running on a computer with a 2 6 GHz i7 processor a 128 GB SSD and 32 GB RAM MFE 21 min 5094 features RFE 48 min 5094 features TFE 8 min 1099 features These times increase by more than thr
6. Click Next Click Browse or type a new folder and path if you want to change the folder location where Profinder is installed Click Next 10 Click Browse or type a new folder and path if you want to change the folder location that Profinder uses by default for your data files You can change the customer data files location only for a new installation of Profinder If other MassHunter software products are installed on the computer Profinder automatically uses the existing default folder location 11 Click Next Profinder Quick Start Guide Install Profinder Batch Targeted Feature Extraction 12 Click Install Agilent Technologies dbk Install to begin the installation Gbk Bade to review on change any of pour iptalabon me tage Check Cannel to ede cht wierd Geer bnabon Pakia Ci Progam Pies gent Mine uraa roras Profinder i O08 Dain Figa Peach C Hiriani 13 Click Finish Agelen Technologies Completed the Agilent MassHunter Profinder Software Setup Gik fe Pirie banton ba ea She baup vizand 14 Click Close to complete Profinder setup Agilent MassHunter Workstation Profinder Software Setup Successtul Profinder Quick Start Guide 31 www agilent com In this book The Agilent G3S35AA MassHunter Profinder Software Quick Start Guide presents the first steps to use the MassHunter Profinder Software Agilent Technologies Inc 2013 Revision A December 2013 G3835 90014
7. efault m di BioConfirmProteinD igest D efault m E Pp BioConfirmS yntheticPeptide D efault m sa Das i di ChomPeakSurvey Default m ee di Default m i GC_QTOF m s di Metabolomics Default m Dekio Profinder Metabolomics m di SamplePurity D efault m Xd Screening Default m a di TestDAReprocessor m Computer i WGF GCMS FbF m 4 WT p Gi File name Profinder Metabolomics m Network Files of type Method Files m 7 Cancel Help Options Save only Qualitative Analysis Method parameters Profinder Quick Start Guide Comments If you have not previously saved your method Save is the same as Save As and prompts you for a name to save your method The Save Method dialog box does not appear when you click Save for your method if you previously saved your method Click Method gt Save As if you want to save your method using a new file name If acquisition parameters exist in the current method you can select whether to also save the acquisition method parameters to the new method 23 Basic Profinder Workflow Save your Profinder project Steps 1 Select Save Project from the menu bar H Agilent MassHunter Profinder 6 06 0 File Edit View Method Wizards H 1 New Project Open Project Save Project as 2 Type the file name and save your This is an optional step You can save your Profinder project including the current sample data
8. the grouping functions to perform properly 17 Basic Profinder Workflow Steps Detailed Instructions Comments 6 Mark the samples to add to your a Mark the samples to add to your e Select a single data file if you are project project in the Show Hide column developing your feature extraction b Click OK method e All of the Sample Files in the same aaea Sampie res project have to have the same Sample file selection and display order polarity If some of the Samples Show Hide Samples Polarity Sample Group have a Positive Polarity and some 1 1_Control_000 d Positive Control have a Negative Polarity then an 1 2_Contral_O00 d Positive Control error message is shown when you 1 3_Control_O00 d Positive Control click OK 1 4_Control_000 d Positve Control 2 1 _Infected_O00 d Positve Infected 2 2 Infeched_O00 d Positve Infected 2 3 Infeched_O00 d Positve Infected 2 4 nfected_O00 d Positive Infected 3 1_Control_250 d Positve Control 3 2 Control 250 d Positve Control 3 3_Control_250 d Positve Control 3 4 Control 250 d Positve Control 4 _ Infected 250 d Positive Infected 4 2 nfeched_250 d Positive Infected 4 3 Infected _250 d Positive Infected 4 4 nfeched_250 d Positive Infected F E F E E E E F F F F F F F F F Add filefs _ Your new project is now begun You are immediately guided to select a feature extraction algorithm and then through the steps to edit and run the
9. Agilent G3835AA MassHunter Protinder Software Quick Start Guide Getting Started 7 User Interface 8 Basic Profinder Workflow 15 Feature Extraction Workflow Algorithms 25 Monitoring your computer while running Profinder 28 Install Profinder 29 What is Agilent Profinder Agilent Profinder software is a stand alone program optimized for batch feature extraction from TOF and Q TOF based profiling data files Feature extraction combined with chromatographic alignment across multiple data files is a critical step in the peak finding and data reduction workflow that minimizes the appearance of both false positive and false negative features by binning the features in the chromatographic time domain Profinder reduces your acquired data size and complexity through the removal of redundant and non specific information by identifying the important variables features associated with the data Careful feature extraction yields a smaller data set that is more easily processed without any compromise in the information quality Profinder is optimized to not only extract features from large data sets but also provides you with an intuitive user interface to inspect and review each feature across the files associated with your data set With Profinder you can review and compare extracted ion chromatograms and mass spectral data associated with each feature Your can save your feature extraction progress to a project to review adjust and re
10. Atard 1S agitens Mactuntes Wwerkution Profeider toftwuare Inctallazion find Liser Liconsa Agresment fig i Please read the folyni keret eqreement coretuly gehen Technologies LEGAL NOTICE PLEASE READ THESE TERMS BEFORE INSTALLING OR OTHERWISE USING THE LCERISED MATERLALS ALL USE OF THESE LCENSED MATORLALS 15 SUIECT TO THE LICENSE TERMS SET FORTH BELOW LICENSED MATERIALS INCLUDES THE SOFTWARE ANY WHOLE OR PARTIAL COMES ANDANT ACOOMPANYING INSTRUCTIONS DOCUMENTATION TECHNICAL DATA IMAGES RECORDINGS AND OTHER RELATED MATDALALS FOR LICENSED MATERIALS DOWN LOO ORA AW UL BIL OH LINE WT steps the terms in the L Agreemers me ac ent cancel Bil Agilent massrunges Workstation Profinder Software Installation Choose destination location r p lern hnedcene Select folder where setup vil A fies ae bent Technodoeers Setup wil inated Agent Mabedunter Worlitaion Profind r Gofheare in the fiering To irinli his foide lice Het To instal to a different fodder chick Browse are select another folder a a ee Choose Customer Data Mies Location Age hen Techrokogers Deen 6 folder for cubtomer soecic fies such os date and methods Da anih Fodder or Gebel G rev fda eth thee oest beatin Click et wher dhe 30 4 Click Next Read the End User License Agreement Mark I accept the terms in the License Agreement in order to continue with the installation
11. amples Add Remove Sample Files Add Remove Sample Files Main Window Display or hide the various tables and results generated by Profinder so you can increase the available display area for your review Main Window 7 Ay al _ MS Spectrum Results Chromatogram Results Compound Groups Jf Compound Details User Interface i Rfi Aetomanicamy Show Commns PA Group WT FI med We Found s 7 10 Feature Coloring Toggle the feature coloring by sample group Feature Coloring JX Color by Sample Group Color by Sample Group Extraction Select the feature selection algorithm you want to review edit and apply to your data set Extraction Wizards E Wizards 3 Main Window The main window see Figure 2 on page 8 is further divided into up to four areas Compound Groups Compound Details Chromatogram Results and MS Spectrum Results that are used to review the results from applying the feature extraction method to your data set Compound Groups The data presented in Compound Groups is organized as a list of all of your extracted features averaged across all of the data files in your project averaged feature information The Compound Groups window shows a table of compound level information for each feature extracted from at least one data file if the data was extracted using Batch Molecular Feature Extraction or for all targeted features if the data was extracted
12. ass CEF files A separate CEF file is instead of measured RT mass for created for each sample data file Exported RT mass value override e The number of CEF files created is c Click At the location of data file for identical to the number of sample Export destination All of the CEF files data files that were extracted in are placed in the same folder your Profinder project containing the sample data files d Click OK Export to CEF maj Export contents Only compounds visible in Compound Groups table All compounds Exported RT mass value overide Export median RT mass instead of measured RT mass Export destination At the location of data file At specified directory MassHunter Data 22 Profinder Quick Start Guide Save your Profinder method Basic Profinder Workflow You save your Profinder feature algorithm method using a unique name Steps 1 Select Save from the menu bar Detailed Instructions Agilent MassHunter Profinder 6 06 2 Type the file name and save your File Edit View Method Wizards ela Automatica Click Method gt Save a Type the name to use for your method method file in the Save Method dialog box b Click Save H save Method x3 Save in di B 06 00 2 F c P BioContirmlntactProtein D efault m PY YGF 7 d BioContirmlntactProteinHighM ass D efault m LN di BioConfirmO ligonucleotideLarge D efault m Recent Items a BioConfirmOligonucleotideS mall D
13. d 7 11 20 A File folder d Two Variable Experiment 2 E i dJ 3 1_Control_250 d 7 11 20 File folder d CEF Files EE f E 3 2_Control_250 d 7 11 201 File folder RAW Files ___ Ep E v d 3 3_Control_250 d 7 11 2013 8 File folder v Filename Two Variable Data X Save as type Profinder project file Profinder Hide Folders Save Profinder Quick Start Guide Feature Extraction Workflow Algorithms Feature Extraction Workflow Algorithms Three feature extraction algorithms are available in Profinder Each extraction algorithm is designed to efficiently extract the features compounds in your sample data files The resulting compound groups are imported into your MPP experiment When you begin a new analysis start with loose feature extraction algorithm parameters and review the results for false positive and false negative features Then adjust the algorithm parameters to reduce the appearance of false positive features without increasing the loss of actual features false negative features Batch Molecular Feature Extraction Profinder Quick Start Guide Molecular feature extraction MFE performs chromatographic deconvolution to find the features in your samples After finding the features the features compounds are aligned across all of the selected sample files using mass and retention time RT After performing MFE Profinder employs an algorithm to re assign ion species using cross file analysis to
14. der Software inciamation Agilent MassHunter Workstation Profinder Software r a User Accoun Contre m Do you want to allow the tollowing program to make changes to this computer Programmame Agilent MassHunter Workstation Profinder Software Vented publsher Agilent Terh skogies Incorporated Fab igeri Hard dimet en bhri computer wr User details Wes Change when there notice ations Profinder Quick Start Guide Install Profinder Install Profinder on the highest performing computer you have available to reduce the time it takes to extract the features from your sample files Profinder requires a computer running Windows 7 64 bit with at least 8GB of RAM Note To significantly improve Profinder performance and to reduce the time needed to extract features from your data sets make sure that your computer has 16 GB or more of RAM and a solid state hard drive Profinder exe to begin installation of Profinder Click Install in the Agilent MassHunter Workstation Profinder Software Installation dialog box 3 Click Yes in the User Account Control dialog box A setup progress indicator appears briefly and launches the Profinder setup wizard 29 Install Profinder Agelen Technologies Welcome to he Agilent Masseunier Werkstation Profinder Software Bate Setup Wizard Tht Setup iced all inated Agian Mahinda Wiorlebation Profineber ioia on piar Gompuber Chek Meat ho birir i Cane bate Be Shun
15. e an Initial Analysis Identify Features Experiment Design Find Features Advanced Operations as Compounds amp Data Acquisition Spectral Features Statistical Data Analysis Identification Statistical Analyses MassHunter Interpretations Qualitative Analysis Pathways i Filtering WILD ERIC BESOE Class Prediction Additional features r GC MS lt ar MassHunter Mass Profiler MassHunter Figure 1 MassHunter Profinder is an optimized feature extraction tool for TOF and Q TOF LC MS data sets The feature extraction performed by Profinder is similar to that performed by the combination of MassHunter Qualitative Analysis DA Repro cessor and MPP Profinder Quick Start Guide Where to Find More Information Profinder Quick Start Guide Online Help Press F1 To get more information about a pane window or dialog box place the cursor on the pane window or dialog box of interest and press F 1 Help Menu Click Help gt Contents to access the contents of the Profinder Help including wizards basic tasks user interface and reference information Help Click Help for information specific to wizards Documents MPP Quick Start Guide Agilent GB835AA MassHunter Mass Profiler Professional Software Quick Start Guide Agilent publication G3835 90009 Revision A November 2012 MPP Familiarization Guide Agilent G8835AA MassHunter Mass Profiler Professional Software Familiarization Guide Agilent publication G3835 90010 Rev
16. ee times gt 3x using a computer with a 2 4 GHz dual core processor a 500 GB 7200 rpm HD and 8 GB RAM Using the Compound Groups Compound Details Chromatogram Results and MS Spectrum Results windows you can edit your results delete a compound group delete abundance from compound details window or chromatogram results window and integrate a peak manually More information is available in the online Help The next steps in this Quick Start Guide help you export your results and save your method Profinder Quick Start Guide Basic Profinder Workflow Export your Profinder features You save the features in your sample data files to a file format called a compound exchange file CEF that is used to exchange data between Agilent software CEF files are used to import your molecular features into Mass Profiler Professional Steps Detailed Instructions Comments 1 Select Export as CEF from the File Click File gt Export as CEF menu am Agilent MassHunter Profinder 6 06 0 Edit View Method Wizards H b Mew Project 7 S Open Project del Save Project Save Project as e Add Remove Sample Files Export as CEF Profinder Quick Start Guide 21 Basic Profinder Workflow Steps Detailed Instructions Comments 2 Export your features compounds a Click All compounds for Export e The features extracted from your to CEF files contents sample data files are exported to b Clear Export median RT m
17. file extraction results so that you can continue reviewing your results and the extraction method at a later time Detailed Instructions e Click File gt Save Project a Type the name to use for your project Comments If you have not previously saved your project Save Project is the same as Save Project as and prompts you for a name to save your project The Save As dialog box does not appear when you click Save Project if you previously saved your project Click File gt Save Project as if you want to save your project using a new file name Note Profinder project pl files can be one GB or more in file size 24 project file in the Save as dialog box b Click Save a H Save as G a MassHunter Data Profinder Two Variable Experiment RAW Files gt v Search RAWFies S Organize v New folder J Downloads Name Date modified Type Size d Hotfix PENS i J 1 1_Control_000 d 7 11 2013 8 30 A File folde dJ Intel OAG 1 2_Control_000 d 7 11 20 File folder J Logs Ses 1 3_Control_000 d 7 11 20 File folder P lotus s hee i 1 4_Control_000 d 7 11 2013 8 33 File folde di MassHunter s REEE gai J 2 1_Infected_000 d 7 11 20 File folder M configuration a 9 4 e dJi 2 2_Infected_000 d 7 11 20 File folder M Data Profinder g j i d 2 3_Infected_000 d 7 11 2013 8 37 File folder di Profinder m s SMe 6 Ji 2 4_Infected_000
18. g the available columns are found in the online Help in the topic Compound Groups Table Columns A list of the available columns is displayed when you right click within the Compound Groups table and then click Add Remove Columns see Figure 4 on page 12 Compound Details The data presented in Compound Details is organized as a list of the appearance of a selected feature compound in all of the data files in your project feature information by data file The Compound Details window shows a table of compound level information for a single feature selected in the Compound Group window The quantitative information is shown for the selected feature as it is found in each data file in your project Information regarding the available columns are found in the online Help Compound Details Table Columns A list of the available columns is displayed when you right click within the Compound Details table and then click Add Remove Columns see Figure 4 on page 12 Chromatogram Results Chromatogram Results presents the extracted ion chromatogram EIC for each feature and for non targeted feature extraction the extracted compound chromatogram ECC for the ions contained in the molecular feature for the feature selected in the Compound Groups window An EIC ECC set is displayed for each data file By default the chromatograms are displayed in an alternating sequence of ten colors to help you review the data for a particular data fi
19. generate compound groups Batch Molecular Feature Extraction Method Extraction Compound Compound Binning Post Processing Parameters Filters and Alignment Filters Step 1 of 4 Step 2 of 4 Step 3 of 4 Step 4 of 4 Compound Charge State Mass Defect Figure 6 Four steps are presented in the Batch Molecular Feature Ex traction Method wizard 25 Feature Extraction Workflow Algorithms Batch Recursive Feature Extraction Recursive Feature Extraction RFE performs MFE as described above and then uses mass and retention time of the results to perform a targeted feature extraction referred to as Find by Ion FbI Using the untargeted MFE results for a targeted FbI feature extraction is referred to as recursive feature extraction After calculating the median mass median RT and composite spectrum from the aligned features found using MFE FbI uses the median values to perform a targeted extraction to improve the reliability in finding the features in your data This recursive feature finding combined with replicate samples in your data set improves the statistical accuracy of your analysis and reduces the potential for obtaining a false positive or false negative answer to your hypothesis The recursive feature extraction workflow performed by Profinder is similar to that outlined in the Agilent Metabolomics Workflow Discovery Workflow Guide The difference is that the feature extraction process happens ina single step
20. gorithm Click Next to edit and review the method for the Feature Extraction algorithm ae eRe ee i ee ie Re ee eg Add sample files Click Method gt f O af Select At the f click File gt Click Finish to run Save to save location of the Export as CEF the Feature your method data file for MPP analysis Extraction Workflow topes to EF Paget cote Urr compord vebis n Coeur Groapa tiie a 4 apard faceted AT mma va ere Eoft feii HTa hki of aard FT ina o Select your B H p ecm i aa Be tearm feature An eed daa Asa a extraction Save your Manis Daia algorithm and Profinder Export your then edit and run method features the method ment Figure 5 The basic Profinder workflow Profinder Quick Start Guide 15 Basic Profinder Workflow Add sample files In this task you launch Profinder select your sample files and add the sample files to your Profinder project Steps Detailed Instructions Comments 1 Start Profinder e Click the Profinder icon i on your desktop or click Start gt All Programs gt Agilent gt MassHunter Workstation gt Profinder B 06 00 2 Begin your Profinder project by e Click File gt Add Remove Sample e Ifyou click File gt New Project adding sample files Files or click Add Remove Sample after starting Profinder you are Files 2 Add Remove Sample Files on automatically prompted to add H Agilent MassHunter Profinder B 06 C the toolbar sample files
21. ision A November 2012 MPP Application Guide Agilent G8835AA MassHunter Mass Profiler Professional Software Application Guide Agilent publication G3835 90011 Revision A November 2012 Mass Profiler Professional User Manual Agilent MassHunter Mass Profiler Professional User Manual Agilent publication January 2012 Discovery Workflow Guide Agilent Metabolomics Workflow Discovery Workflow Guide Agilent publication 5990 7067EN Revision B October 2012 Discovery Workflow Overview Agilent Metabolomics Workflow Discovery Workflow Overview Agilent publication 5990 7068EN Revision B October 2012 Integrated Biology Workflow Guide Integrated Biology with Agilent Mass Profiler Professional Workflow Guide Agilent publication 5991 1909EN Revision A June 2013 Integrated Biology Workflow Overview Integrated Biology with Agilent Mass Profiler Professional Workflow Guide Overview Agilent publication 5991 1910EN Revision A June 20138 Qualitative Analysis Familiarization Guide for LC MS Agilent MassHunter Workstation Software Qualitative Analysis Agilent publication G3335 90146 Revision A October 2012 Quantitative Analysis Familiarization Guide Agilent MassHunter Workstation Software Quantitative Analysis Agilent publication G3335 90152 Revision A February 2013 Training Road Show Slide Presentation Metabolome Analysis From Sample Prep Through Data Analysis Metabolomics Road Show March 2011 Training Cour
22. le as you select different features 11 User Interface MS Spectrum Results MS Spectrum Results presents the ent alv aa oe ___ _ averaged mass spectrum MS across the integrated ECC for the st 7 feature selected in the Compound Groups window for each data file By default the MS is displayed in an alternating sequence of n ten colors matched with the Chromatogram Results to help evs Cod amp ESI MFE Spectrum 5 002 5 966 min FrageI750V 4 2 coso YOU review the MS data for a particular data file as you select zie different features l Maps f i 127 15 te x18 Cod amp EY MFE Spectrom 524 6030 min Frege 1750 1 3 Contra 00 15 apa i E Pal Cede ES MFE Spectro 5 225 5 000 min Frege 15 0 1A Control M hal Z 2134100 13 1 05 2 io aa Shortcut menu commands A right click in any of the main windows shows you a menu of options Figure 4 applicable to where you click and to your current selection Options available include customize the columns in the table views copy to the system clipboard and delete compound groups or individual compounds Delete Compound Group s Extract Manual Compound s Copy to Clipboard Add Remove Columns Delete Compound Abundance s Hide Empty Columns Copy to Clipboard Automatically Show Columns with Data Copy to Clipboard Compound Groups Chromatogram MS Spectrum Compound Details Results Results Delete Compou
23. le name 1 1_Control_000 d 1 2_Control_000 d 1 3_Contn Files of type Data Fies o Files d Cancel Cancel Add Remove Sample Files Sample file selection and display order Show Hide S SI E r am Samples 1 1_Control_000 d 1 2_Control_000 d 1 3_Control_000 d 1 4_Control_000 d 2 1_Infected_000 d 2 2 Infeched_O00 d Profinder Quick Start Guide Polarity Positive Positive Positive Positive Positive Positive Help Click the data entry cell under the Sample Group column next to the sample file name Enter the group identification text Repeat for each sample file Sample Group Control Control Control Control Infected Comments Selected sample data files are highlighted in the Open file dialog box If you are just starting to become familiar with feature extraction you may want to select a single data file Selecting a single data file reduces the time it takes Profinder to perform your feature extraction and to display the results for your review After you have developed your feature extraction method and applied it to one or more sample data files you can click Add Sample Files select your entire data set and rerun feature extraction When the data entry cell is selected it is initially highlighted using a background color When entering Sample Group names the entries must use identical letters numbers punctuation and case in order for
24. nce O Pet ounce Menita File Mienia Heli Overeirw cpu Memory Disk Network ee Foose WB iiss used Pryocai Memory oe as image PD Han faa Comm Weeting Shaman Prue dg elirec soe eet o eet a3 752 76 258 TER Sat enn pa LH agi 4 LH Be bi 55a 2110H ipiiris ait 4105 ae A I TE mapa 478 o Eber bs TLI 1549 ar70 Lissa Ba at Lise a alzi SIS a2 SE Tae r 741s TERT wa Baa m4 moiit gieti i 6 43400 a La 378 m53 40 Serres or a kt 4H a Pate ISIH i1534 PEET Cammit Charge iori titania Minne ave Fra pi i mii Ligal ioiai am o MM 45853 NM OMH Physical Mesrusy MB 620 6 in ue DT 28370 MB vaias A ti L u m E Hantwar W in use E Moanities E itanaicy E Free Hard Faullaties 1 Resend 420 Me a1 ME J207 MU 2363 ME LI MB Araillable 28970 ME Cached 355A ME Total J241 BIB Inilalled 32768 ME Windows Tack Manager ees lt lt File Optiens View Help Applications Processes Services Performance ietenrling Liners PU Wage OPU Usa Fito Memary Physiral Memary Lange Heriary Pirpeical Memory MB Syslem Total 41 Handles 24305 Cached 3559 Threads Erat Avalabie J094 Procestes ai Free 25456 Up Tire O 00308 Commit Gu aj dz Kernel Memory Mol Pager H5 Hraaged iz Frocestes S TPU Usage 14 Pinaral Memen 11 Figure 9 Monitoring the system and memory resources on your com puter Profinder Quick Start Guide Install Profinder Agilent MUnHunter Workitabion Profin
25. nd Abundance s Del Add Remove Columns Hide Empty Columns Automatically Show Columns with Data Copy to Clipboard Figure4 The shortcut menu commands available within the main window automatically adjust based on the active area 12 Profinder Quick Start Guide User Interface Definitions Algorithm An algorithm is a set of automated sequential mathematical tasks performed to find filter align and extract features from your chromatographic mass spectral data sets Feature A feature is synonymous with compound A feature is referred to interchangeably with compound molecular feature element or entity during the various steps of analysis using Agilent MassHunter software Method A method is a set of parameters that are associated with the three feature extraction algorithms used by Profinder Methods containing the parameters for the algorithms can be saved using unique file names Wizard A wizard is a sequence of interactive steps used by Agilent MassHunter software to guide you through the steps necessary to complete an analytical task Profinder uses a set of wizards to guide you through the parameters associated with each feature extraction algorithm Workflow A workflow is an Agilent document or a graphical overview that captures a sequence of steps to guide you through an analytical task A workflow may cover more than one wizard and may include steps performed by more than one Agilent MassHunter software prog
26. process at a later time Agg Agilent Technologies The feature files generated by Profinder can be imported into Agilent Mass Profiler Professional MPP a powerful chemometrics platform used in any MS based differential analysis to determine relationships among two or more sample groups and variables Features of Profinder e Open all of the files associated with your Agilent TOF and Q TOF LC MS data set sample files in a single selection process e Create methods for your feature extraction and chromatographic alignment by following a guided step by step wizard for the selected algorithm e Choose from three feature extraction algorithms Molecular Feature Extraction Recursive Feature Extraction and Targeted Feature Extraction e Extract the features from all of the data files in your data set by running a single algorithm e Automatically generate an extracted ion chromatogram EIC and extracted compound chromatogram ECC for each feature found in each data file e Review your features and chromatographic alignment using an intuitive graphical interface e Delete false positive features from your results e Export your extracted features via two file formats Compound exchange format CEF is a file format that is used to exchange data between Agilent software CEF files are imported into MPP for statistical analysis Comma separated value CSV is an ASCII text file that is readily imported into text editors and
27. ram Help Online Help and detailed information regarding the various fields and statistical treatments are available by pressing F1 clicking Hep or clicking Help gt Contents from the menu bar Profinder Quick Start Guide 13 User Interface 14 Unsaved parameter changes When you make a change to a parameter in Profinder the software automatically places a change icon A a blue triangle shape in the wizard tab and next to the value containing the parameter where you made a change This icon indicates that you have unsaved parameters changes and helps you remember to save the changes you have made to the method The original parameter value may be viewed by placing your pointer over the change icon When you save your method the change icons disappear Profinder Quick Start Guide Basic Profinder Workflow Basic Profinder Workflow The basic Profinder workflow guides you through the steps necessary to extract features from your sample files The steps shown in Figure 5 are described in the following sections e Add sample files on page 16 e Select your feature extraction algorithm and then edit and run the method on page 19 e Export your Profinder features on page 21 e Save your Profinder method on page 23 e Optional Save your Profinder project on page 24 Basic Profinder Workflow Click File ET ERR Select a Feature ace T Click Open 7 Click OK fee Extraction Workflow al
28. ses Visit www chem agilent com to view a listing of training courses for MPP Profinder Quick Start Guide Getting Started Getting Started How do get started Profinder Quick Start Guide This Quick Start Guide helps you install Profinder review the Profinder user interface and perform feature extraction using your data 1 Install Profinder Follow the instructions in Install Profinder on page 29 Launch Profinder Double click the Profinder icon located on your desktop or click Start gt All Programs gt Agilent gt MassHunter Workstation gt Profinder B 06 00 Review the following three sections in this Quick Start Guide User Interface on page 8 Basic Profinder Workflow on page 15 Feature Extraction Workflow Algorithms on page 25 Review the Discovery Workflow Guide see Documents on page 5 This guide helps you improve your results by covering topics that help you Prepare for an experiment Explain the parameters related to finding features Perform an initial differential analysis using MPP Extract the features in your samples following the example Basic Profinder Workflow see Basic Profinder Workflow on page 15 User Interface User Interface A feature may be referred to as a compound molecular feature element or entity during the various steps of analysis using Agilent MassHunter software Help and detailed information regarding the various parame
29. spreadsheets e Save your feature extraction parameters as Profinder methods e Save your feature extraction progress as a Profinder project file and open the project at a later time to review adjust and reprocess your data files Profinder Quick Start Guide Where is Profinder used in your experiment Profinder Quick Start Guide Profinder is used to extract the features from LC MS data files you acquired from your experimental samples An untargeted differential analysis experiment may include eight steps as shown below Profinder is used in step three 1 ow oOo cil A GW N Prepare for your experiment Acquire your data Data Acquisition Extract the spectral features Profinder Import and organize your data MPP Create your initial analysis MPP Identify features in your data ID Browser Save your project MPP Perform advanced analysis operations MPP Figure 1 shows the steps and Agilent tools that are used in an untargeted differential analysis The feature finding steps performed by Profinder can alternatively be accomplished using a sequence of steps involving MassHunter Qualitative Analysis DA Reprocessor and MPP as described in the Agilent Metabolomics Workflow Discovery Workflow Guide Workflow for a Differential Analysis Prepare for an Experiment Experiment Design Hypothesis Natural Variability Replicate Sampling System Suitability Sampling Methodology Import and Organize Data Creat
30. ters and statistical treatments are available when you press F1 or click Help gt Contents from the menu bar Main Functional Areas The main Profinder window consists of three parts 1 the Menu Bar 2 the Toolbar and 3 the Main Window The main functional areas are shown in Figure 2 Main Window ES Aubomaticath A eros Ho data to depis Compound Groups Table of compound level information MS Spectrum Results Chromatogram Results interactive views for your mass Interactive views for your spectral results including any chromatogram results associated structural information if available r _ DD No data to depim Compound Details Table of information about each compound Figure 2 The main functional areas of Profinder as viewed before you begin a project 8 Profinder Quick Start Guide Profinder Quick Start Guide User Interface 1 Menu Bar The menu bar Figure 3 provides actions that are used for managing your projects methods display and extracting features File Edit View Method Wizards Help Figure 3 Menu bar 2 Toolbar The toolbar is located below the menu bar and contains five groups of buttons for commonly used tasks Project New project Open project and Save project Project New Project es ki Save Project Open Project Samples Add sample files to your new or current project s
31. ures consist of mass and retention time instead of molecular formula FbF calculates reasonable isotope patterns and uses these patterns with retention time tolerances to find the target features in the sample data files When the input molecular features are filtered from a find process that was previously untargeted the molecular features found using Find Compounds by Formula is also referred to as recursive finding Batch Targeted Feature Extraction Method ae Mate hing EIC Peak Spectrum l Sots Tolerances and Integration and Extraction and sia oe ae Ste s of 5 Scoring Filtering Centroiding j Step E of 5 P Step 2 of 5 Step 3 of 5 Step 4 of 5 ie Formula i Positive lons Scoring Smoothing Ceniroiding Figure 8 Five steps are presented in the Batch Targeted Feature Ex traction Method wizard Profinder Quick Start Guide 27 Monitoring your computer while running Profinder Monitoring your computer while running Profinder 28 You can monitor your computer s resources especially memory while running Profinder Right click on the computer taskbar and then click Start Task Manager to launch the Windows Task Manager Select the Performance tab to monitor your CPU and memory usage For additional details regarding your computer s memory usage click Resource Monitor and select the Memory tab See Figure 9 If your memory usage approaches the amount of physical RAM adding additional RAM increases performa
32. using Batch Targeted Feature Extraction Quantitative information is shown as the average value for the feature across all of the files where the feature was found A compound group is a single compound feature found in any one or more of the data files in a project For example if the first data file in the project yields 35 compounds then at least 35 compound groups are in the project If additional unique compounds are found in the other data files then additional compound groups are created Profinder Quick Start Guide f EE Astomatically Show Columns Fal Files TE Sowe MFE TE wpm TE AT 11_Ceeenl 000d 10 1302 Ti oyd cr 100 es iF 1 3 Cortial 000d 10 Tedd 1 4_Comtrel_000 4 100 T 2a EI infected 000 4 Te EFA D inlecied Mid 10 EFA a Infeeted_ Od 1 it z infected OOO Toe EEFE como 20d OA AS J2 Cora 250d 1 19023 Contrel 250d Ere J4 Cobol Jd 1 wa _Inineied_ 25d 1 750 Re 42 infected 250d w eure 4 3_Inbected_2o0 d 100 dd Inema 250d an T Pate ive tiQbwiaie aio s zige ES ESC 191 1150 1921258 1931243 7131128 i 1 A J Sean Fragai 7S OV 1 i 0 EJ EAVES VR TAJ T246 214110 2 Scan Frage Tso 1 i nA e s10 seo E191 ee TALI 20 VR 274 1111 Sean Frage 50 1 iD z aiD E EKA131 1TA0 VAL TS T1168 21310 1 Scan Frage 1 500 1 Profinder Quick Start Guide User Interface Information regardin
Download Pdf Manuals
Related Search