Agilent G3835AA MassHunter Mass Profiler Professional Software
Contents
1. l Do not show this dialog again SS Lol Gg 20 Mass Profiler Professional Quick Start Guide Basic Tasks Steps Open existing project 3 Open an existing project in the Startup dialog box and select the Malaria project from the list of all of your existing projects Detailed Instructions Startup dialog box in Step 2 on page 20 b Click OK the Open Project dialog box d Click Open E Open Project E Name Creation Date Modified Date Owner x Malaria Sat May21 141 5at May21 141 Displaying results from 1 to 1 of 1 Showing page 9 f Cl of a ep Create new project 4 Create a new project in the Startup dialog box and import the experiment stored in the Malaria project into the new project Fe el a Click Create new project in the Startup dialog box in step 2 on page 20 b Click OK Click Open existing project in the Select the Malaria project row from Comments e Open existing project allows you to open a project that is no longer displayed in the recent project list e Open existing project opens the project and the experiment s that are stored in the project e When you have a large number of existing projects on your computer you may have to use the page navigation buttons in the Open Project dialog box e A selected project is highlighted by a color based on your PC s system settings e You can now u2. Designed for both mass spectrometrists and statisticians with guided and advanced workflows Provides comprehensive statistical tools including ANOVA PCA volcano plots hierarchical trees SOMs QT clustering and five different methods for class prediction Generates inclusion lists for subsequent MS MS based analyses to facilitate identification of compounds of interest The ID Browser allows integrated identification and annotation of compounds using LC MS Personal Compound Databases METLIN Pesticides Forensics and GC MS libraries NIST and Agilent Fiehn Metabolomics Allows import and export of data in several formats e g to further extend and customize statistical analysis and visualization capabilities using R Scripts Integrates smoothly with Spectrum Mill to enable TOF Q TOF based discovery and QQQ based verification of protein biomarkers Integration with GeneSpring allows the correlation of pathways between MS metabolomics proteomics and microarray data transcriptomics in one project enabling true integrated biology studies Class prediction models from GC MS LC MS CE MS and ICP MS data now can be used with the new standalone Automated Sample Class Prediction software to enable high throughput routine classification of unknown samples Mass Profiler Professional Quick Start Guide What s new in MPP 13 0 e New analytical capabilities Correlation analysis between pairs of entities or samples in an expe
3. Mass Profiler Professional License Activation x Select License Type Please choose your license type Individual license G Order ID You should have valid OrderlDs to activate Mass Profiler Professional over the web To get OrderlDs write to the support team at informatics_support agilent com _ Mass Profiler Professional Order _ GeneSpring GX OrderID _ GeneSpring NGS Order _ Pathway Architect OrderID Example ABC1 2345 6789 Proxy settings _ Use proxy Figure 1 Mass Profiler Professional License Activation dialog box Mass Profiler Professional Quick Start Guide 7 Getting Started Moving a License MPP licensing is automatically enforced You may move a license to another computer by surrendering it on the current computer and then activating it on the new computer If you need to uninstall MPP it is always best to surrender the existing license before un installing MPP so that the license is available to be moved to another computer To surrender your license 1 Click Help gt License Manager in the menu bar Help Help Documentation Index Contact Technical Support GeneSpring Extras Update Product gt Install IDBrowser About Figure 2 License Manager is available from the Help menu 2 Click Surrender in the License Manager dialog box Pllicense Manager x Order ID Order ID Available Total Samples Mass Profiler Professional 1234 1234 1234 UNLIMITED UNLIMITED GeneS
4. quaunsadsey ajqenea om AW EE RIETS Ace Eeg dEr det won suo nejouuy pol ma et paloi JUJWHJdKJ ET OM ENT GT TGTE Seel 11 Mass Profiler Professional Quick Start Guide User Interface 12 ee Figure 9 on page 11 is further divided into five areas the Project Navigator the Experiment Navigator the Desktop Area the Workflow Browser and the Legend Project Navigator Displays the current project and lists all the experiments with the project Experiment Navigator Displays information related to Samples Interpretations Analysis and My Favorites in folders related to the selected experiment in the Project Navigator Each experiment within a project has a separate experiment navigator window Desktop Area Display of one or more interactive views associated with the experiments Each view in the desktop area is marked with a tab and you can configure each view separately Click Windows gt Tile to arrange multiple views on the desktop The current experiment interpretation and analysis is noted using bold font in the Project Navigator and Experiment Navigator A right click anywhere in the active view shows you a menu of options Figure 10 to customize the view copy the view to the system clipboard and export the view as an image file bmp jpg jpeg png and tiff or as an HTML file Zoom Mode Reset Zoom Copy View Export As Trellis Catview Color By Yenn Properties
5. Figure 10 Selection Mode Invert Selection Clear Selection Limit To Selection ort Colt it Ctrl C Select All Rows Invert Row Selection Clear Row Selection Limit To Row Selection The right click available options within the desktop view automatically adjust to the type of view Mass Profiler Professional Quick Start Guide User Interface Workflow Browser The Workflow Browser left is organized into sequential groups of operations for the analysis of xperiment Setup Quick Start Guide your data Experiment Setup Quality Control ee Analysis Class Prediction Results Interpretations TE eee Pathway Analysis optional NLP Networks Quality Control i ages ona a O p t 4 O nN al an d Utiliti e S Filter by Frequency Wor klo yy Create Interpretation Filter on Sample Variability Filter by Flags Filter by Abundance Filter by Annotations Analysis Statistical Analysis Filter on Volcano Plot Fold Change Clustering Find Similar Entities Filter On Parameters Principal Component Analysis Find Minimal Entities Class Prediction Build Prediction Model Run Prediction Run Prediction from file Export Prediction Model Results Interpretations Find Similar Entity Lists Export for Recursion IDBrowser Identification Export for Identification Export Inclusion List Import Annotations Pathway Analysis Single Experiment Analysis Multi Omic Analysis Launch IPA Export to MetaC
6. and produce an initial differential expression for your analysis The Significance Testing and Fold Change Wizard flow diagram is illustrated in Figure 15 The Mass Profiler Professional Familiarization Guide p n G3835 90010 see Documents on page 4 guides you through an initial differential analysis using the Malaria Demo data Mass Profiler Professional Quick Start Guide Basic Tasks Flow Chart of the Analysis Significance Testing and Fold Change Wizard r Filter by Frequency Step 5 Experiment Quality Control on Grouping Samples Step 6 Significance Analysis Go to Step7 Fold Change Step 8 ID Browser Identification V Save your project and perform advanced tasks Figure 15 Analysis Significance Testing and Fold Change Wizard Mass Profiler Professional Quick Start Guide 19 Basic Tasks Open a recent or existing project When you start Mass Profiler Professional the Startup dialog box allows you to quickly open a recent project an existing project on your computer or import an experiment from an existing project into a new project The steps presented are recommended if you are already familiar with the operations available in the Workflow Browser If you are new to using Mass Profiler Professional start with Set up a new project on page 15 and then refer to the Mass Profiler Professional Familiarization Guide p n G3835 90010 see Documents o
7. e experiment with new data or previously imported data Choose Experiment f Open existing experiment button or click the Add experiment UD button If you click Open existing experiment you are prompted for the experiment to add to the project as described in Open a recent or existing project on page 20 16 Mass Profiler Professional Quick Start Guide Basic Tasks Steps 5 Type and select information that a guides the experiment creation in the New Experiment dialog box x Detailed Instructions Type the descriptive name Malaria demo in Experiment name This name may be different from the project name Select Mass Profiler Professional for Analysis type Select Unidentified for the Experiment type Select Analysis Significance Testing and Fold Change for Workflow type TypeMalaria LCMS ESI pH 7 in Experiment notes Click OK Comments Experiment type determines how Mass Profiler Professional manages the data Unidentified is the proper Experiment type selection when the compounds have only been identified by their molecular features of neutral mass and retention time Identified is the proper Experiment type selection when the compounds have been identified by compound formula and or CAS number Combined Identified Unidentified is the proper Experiment type when you are unsure if the data has been identified in full or in part or when MassHunter Qualitative Analysi
8. Agilent G3835AA MassHunter Mass Profiler Professional Software Quick Start Guide Getting Started 6 User Interface 10 Basic Tasks 15 Advanced Tasks 24 Acknowledgment and Citations 24 What is Agilent Mass Profiler Professional Agilent Mass Profiler Professional MPP software is a powerful chemometrics platform designed to exploit the high information content of mass spectra MS data and can be used in any MS based differential analysis to determine relationships among two or more sample groups and variables MPP provides advanced statistical analysis and visualization tools for GC MS LC MS CE MS ICP MS and NMR data analysis MPP also integrates smoothly with Agilent MassHunter Workstation Spectrum Mill and ChemStation software and is the only platform that provides integrated identification annotation of compounds and integrated pathway analysis for metabolomic and proteomic studies The system also enables Automated Sample Class Prediction that revolutionizes mass spectrometer based qualitative analysis of unknown samples in many applications MPP is ideally suited for applications characterized by complex sample matrices such as metabolomics proteomics natural products food beverages flavors fragrances and environmental analyses E Agilent Technologies Features of Mass Profiler Professional Allows differential analysis of two or more sample sets from one or multiple MS analysis platforms in a single project
9. Professional Quick Start Guide Basic Tasks Basic Tasks Set up a new project A project is a container for a collection of experiments each experiment contains your samples interpretations and analyses A project can have multiple experiments on different sample types and organisms Create a new project and experiment for your data A new project and experiment is created through four sequential dialog boxes 1 Startup 2 Create New Project 3 Experiment Selection and 4 New Experiment The Agilent Malaria Demo data supplied with MPP is used as an example in each step You may substitute the malaria information with information for your data Steps Detailed Instructions Comments 1 Start Mass Profiler Professional a Click the Mass Profiler Professional The Startup dialog box helps you icon fal on your desktop or click quickly set up a new project this Start gt All Programs gt Agilent gt section or continue your analysis MassHunter Workstation gt Mass with a previous project see Open Profiler Professional gt Mass Profiler a recent or existing project on Professional page 20 2 Create a new project from the a Click Create new project e Create new project provides you Startup dialog box b Click OK with the option to create a new experiment or import an experiment from an existing project ea xl into the new project Welcome to MassProfiler Pro i e After closing an n project Select wh
10. at you would like to do from the options below then dick on OK SES P OPE yOu to continue may create a new project from the Menu bar click Project gt New Project or from the Toolbar click eo the New project button Open recent project Selectrecent project New Project IT Do not show this dialog again ep Mass Profiler Professional Quick Start Guide 15 Basic Tasks Steps Detailed Instructions Comments 3 Type descriptive information inthe a lypeMalaria Project in Name New Project Details section ofthe b TypeProject containing the The project name and notes may be viewed and edited at any time Create New Project dialog box Agilent Malaria Demo in using the Project Inspector by Notes clicking Project gt Inspect Project c Click OK from the menu bar E create new Project n E create new Project n New Project Details New Project Details Notes er EH Lal zs 4 Create a new experiment in the a Click Create new experiment e You may create or add a new Experiment Selection Dialog b Click OK experiment to your project from the dialog box Menu bar click Project gt New Experiment or from the Toolbar x eege 4n experiment is an organized collection of LEMS or GCIMS sample data from a given data source IF you have an experiment you wish to use From a previous project please choose Open existing experiment You may also create a new
11. by the steps to create an initial analysis 17 Basic Tasks 18 Import your data using the MS Experiment Creation Wizard After you set up a project and create an experiment the MS Experiment Creation Wizard guides you through the necessary steps to organize your experiment import your data define your experiment variables and prepare your data for analysis The MS Experiment Creation Wizard flow diagram is illustrated Figure 14 The data preparation includes grouping filtering alignment normalization and baselining The Mass Profiler Professional Familiarization Guide p n G3835 90010 see Documents on page 4 guides you through importing and organizing the Malaria Demo data See the Mass Profiler Professional Application Guide p n G3835 90021 for details to import non Agilent data Flow Chart of the MS Experiment Creation Wizard Experiment Grouping Sample Summary Select Data Source Step 2 Step 10 Select Data to Normalization Import Criteria Steps 3 amp 4 skipped Step 5 Step 11 Sample Reordering Baselining Options Goto Step6 Create an initial analysis Figure 14 MS Experiment Creation Wizard Perform your initial differential analysis using the Analysis Significance Testing and Fold Change workflow The Significance Testing and Fold Change Wizard guides you through the steps necessary to enter parameters and values that improve the quality of your results
12. ct All the contents of the experiment will be exported and can be imported later Sequencing experiments and MOA experiments with a sequencing experiment as input are disabled and cannot be exported Jh Differentiation by Infection and Treatment d Select or create the file folder e Type the File name f Click Save Mass Profiler Professional Quick Start Guide 23 Advanced Tasks Advanced Tasks The operations available in the Workflow Browser see Figure 11 on page 13 provide the tools necessary for analyzing features from your mass spectrometry data depending upon the need and aim of the analysis the experiment design and the focus of the study This helps you create different interpretations to carry out the analysis based on the different filtering normalization and standard statistical methods Follow the procedures in the Mass Profiler Professional Familiarization Guide p n G3835 90010 and Mass Profiler Professional Application Guide p n G3835 90021 see Documents on page 4 for increasingly detailed information to help you use MPP The Agilent Metabolomics Workflow Discovery Workflow Guide p n 5990 7067EN and the Agilent MassHunter Mass Profiler Professional User Manual see Documents on page 4 provide you with techniques and explanations to perform advanced analysis tasks Acknowledgment and Citations 24 BioCyc Pathway Genome Databases Includes BioCyc Pathway Genome database
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14. ed entity and Import entity list from file Plots Statistics and Pathways section Scatter plot Profile plot Histogram plot Matrix plot Venn diagram plot Box and whisker plot Heat map plot Data spreadsheet Summary statistics Create new pathway and Select data source for plots Sidebar section Hide or show the sidebars that contain the Project Navigator Workflow Browser and Legend Project Experiment Entity List Plots Statistics and Pathways sakes HEE BAER i E co e ea E A e E e gt Figure 8 Toolbar Mass Profiler Professional Quick Start Guide User Interface E eet jo wot POW 3531 pue ping VOS ze Sunnud rot o8ed y UO DoaIgIOI ST AIDS STU 210N BIEMIOS JAIN 24 JO Sease jeuoNOUNy urew y 6an P3935 0 tritt Buejdsig sa 5 jiy OESCH UO paypune abuey pjod pue unsa eoueryubis pi HES ie ee Sanyed E r Buet Yum sannua SAWY au Z Z JUTT Z uo n UODTZ E UOD T E UODTp T UODTE T UODTZ T mont Su 0 6l open Aow w npa10 ues abequeb s nan GIN eA suoneey penxa y 91 9 JOUUOW Asowauw e pue 2607 000 10 4u03 1 1 g 40 0 jom Pazyeuuon 2607 301d aoad puebo aea M IA JUUNI BY 0 Payejas UONEWIOJU m PETHEN eg smes Main JUUNI BU ade3sojA gt 0 Deuu07 eege 0 pojejal Aen 10 09 Yar pune SISAIPUY IWO ANW sisAjeuy auto auis Kr sisdjeuy Aemuied suonezouuy yodwr 3st uoisnjauy wodxa d uonesynuap 404 e
15. er Operation Suc ul x Ci Your license has been surrendered successfully Figure 6 Automatic Surrender Operation Successful dialog box 7 Activate your license Order ID on the new computer see Activating a License on page 7 8 Optional Click Start gt All Programs gt Agilent gt MassHunter Workstation gt Mass Profiler Professional gt Uninstall to remove MPP from the current computer Mass Profiler Professional Quick Start Guide 9 User Interface User Interface 10 Note Help and detailed information regarding the various fields and statistical treatments are available by pressing F1 or by referring to the Mass Profiler Professional User Manual Main Functional Areas The main functional areas of Mass Profiler Professional are shown in Figure 9 on page 11 The main MPP window consists of four parts 1 the Menu Bar 2 the Toolbar 3 the Display Pane and 4 the Status Bar 1 Menu Gar The menu bar Figure 7 provides actions that are used for managing your projects experiments pathways and display pane views Project Search View Tools Annotations Windows Help Figure 7 Menu bar 2 Toolbar The toolbar Figure 8 is located below the menu bar and contains five sections of buttons for commonly used tasks Project section New project Open project and Close project Experiment section New experiment and Add experiment Entity List section Create entity list from selection Inspect select
16. k Help gt Documentation Index to access the release notes quick start guides and HTML and PDF versions of the Mass Profiler Professional User Manual Documents Mass Profiler Professional Mass Profiler Professional Familiarization Guide p n G38835 90010 Mass Profiler Professional Application Guide p n G3835 90021 Agilent MassHunter Mass Profiler Professional User Manual You can find a PDF copy in the MPP installation folder C Program Files Agilent MassHunter Workstation Mass Profiler Professional docs manual Workflow Guides and Overviews Agilent Metabolomics Workflow Discovery Workflow Guide p n 5990 7067EN Agilent Metabolomics Workflow Discovery Workflow Overview p n 5990 7068EN Integrated Biology with Agilent Mass Profiler Professional Workflow Guide p n 5991 1909EN Integrated Biology with Agilent Mass Profiler Professional Workflow Guide Overview p n 5991 1910EN Class Prediction with Agilent Mass Profiler Professional Workflow Guide p n 5991 1911EN Class Prediction with Agilent Mass Profiler Professional Workflow Overview p n 5991 1912EN Mass Profiler Professional Quick Start Guide MassHunter Qualitative and Quantitative Analysis e MassHunter Qualitative Analysis Familiarization Guide for LC MS e MassHunter Qualitative Analysis Familiarization Guide for GC MS e MassHunter Quantitative Analysis Familiarization Guide Training Road Show Slide Presentation Metabolome Analysis F
17. n page 4 Steps Detailed Instructions Comments 1 Start Mass Profiler Professional a Click the Mass Profiler Professional MPP begins with the Startup icon Io your desktop or click dialog box to help you quickly open Start gt All Programs gt Agilent gt a previous project MassHunter Workstation gt Mass Profiler Professional gt Mass Profiler Open recent project go to Step 2 Professional Open existing project go to Step 3 b Go to Step 2 Step 3 or Step 4 Create new project go to Step 4 and import an experiment from a previous project Open recent project a Click Open recent project e Open recent project opens the 2 Open a recent project in the b Select Malaria from the Select recent project and the experiment s that Startup dialog box and select the project list are stored in the project If your Malaria project from the recent c Click OK project is not shown in the Select project list recent project list go to Step 3 and select it from the list of existing projects on your computer E ject i i a x e A project is a container for a Welcome to MassProfiler Pro Select what you would like to do from the options below then cick on OK collection of ex BEER ts A proje ct to continue can have multiple experiments on Seen different sample types and Create new project organisms e You can now use the operations available in the Workflow Browser Select recent project Malaria D
18. ons available in the Workflow Browser Modified Date EE Muon Variable Expe Tue Dec T 2 Tue Dec 27 21 3 My Two Variable Expe Weg Dec wed Dec 28 21 3 Differentiation by Inter Sun OC 14 1 Sun Oct 14 Eer Malaria Demo Mon Dec 19 Mon Dec 19 11 3 Differentiation by Infec Fri Jun 22 15 Fri Jun 22 15 41 Differentiation by Infec Fri Jun 22 17 1 Fri Jun 22 17 52 Displaying results From 1 to of 7 Showing page CS fi F of 1 Help Cancel 22 Mass Profiler Professional Quick Start Guide Save your project Basic Tasks Save your current analysis as a TAR file for archiving restoration of any future analysis to the current results sharing the data with a collaborator or sharing the data with Agilent customer support Steps 1 Export your project to a TAR file Detailed Instructions Comments a Click Project gt Export Project ElmMass Profiler Professional Differentiation by Infection and Treatment Search view Tools Annotations Windows Help New Project al Fe a E g Open Project Recent Projects Import Project Inspect Project nd Treatment Close Project Delete Project Share Project Export project as tar archive Change Project Owner Refresh Project New Experiment Add Experiment Exit Chr b Mark the check box next to the experiment you wish to save c Click OK ElChoose Experiments x Select experiments to export with the proje
19. ore Connect to Cytoscape NLP Networks NLP Network Discovery MeSH Network Builder Extract Relations via NLP Utilities Remove Entities with missing signal values Analysis Significance Testing and Fold Change Class Prediction Build and Test Model Figure 11 Workflow Browser operations Mass Profiler Professional Quick Start Guide 13 User Interface 14 Legend The Legend Figure 12 shows the key scale to the use of color in the active desktop view Right click on the Legend window to copy and export the legend as described in the Desktop area Legend Profile Plot Color By 3 4_pH7_pos_01 lg2 19 6 0 1 20 9 x Figure 12 Legend 4 Status Bar The status bar Figure 13 has three informative areas the Status Area the Ticker Area and the Memory Monitor Status Area Displays high level information of the current view such as the number of rows and columns in table views and the number of entities or conditions selected in plot views Ticker Area Displays the coordinates of the cursor in active plot views or the entity identification and value in table views Memory Monitor Displays the total memory being used and the total memory allocated by MPP You can click the Garbage Can icon if at any time to reduce the memory usage Status Area Ticker Area Memory Displaying 941 9 selected 1 15 05 3 4 pH7_pos_ seMof 109 TH co Figure 13 Status Bar Mass Profiler
20. pring GX l 1234 1234 1234 l UNLIMITED UNLIMITED Pathway Architect 1234 1234 1234 UNLIMITED UNLIMITED Surrender Add Change Re activate Modules Module License Status Updates Status Mass Profiler Professional Expires On 12 Apr 2013 Expires On 18 Mar 2013 GeneSpring GX Expires On 12 Apr 2013 Expires On 18 Mar 2013 GeneSpring NGS Not Licensed No Updates Pathway Architect _ Expires On 12 Apr 2013 Expires On 16 Mar 2013 ox Figure 3 License Manager dialog box 3 Mark Mass Profiler Professional and any additional product Order IDs to surrender 4 Click OK Mass Profiler Professional Quick Start Guide Getting Started x Choose the products orderIDs to surrender Choose Product JV Mass Profiler Professional JV GeneSpring GX Iw Pathway Architect Col ES Figure 4 Order ID surrender product selection dialog box 5 Click Yes in the Confirm Surrender dialog box Because your license is no longer active on the current computer MPP software immediately closes when you click OK Confirm Surrender xj This operation allows you to use the application with the same Orderld on another computer Are you sure you want to surrender the license i No Figure 5 Confirm Surrender dialog box 6 Click OK in the Automatic Surrender Operation Successful dialog box Because your license is no longer active on the current computer MPP software immediately closes Automatic Surrend
21. riment or in a multi omic experiment Metadata Framework to view sample metadata in conjunction with the clustered experiment results Support for KEGG pathways in single experiment as well as multi omic pathway significance analysis PLS DA algorithm displays the R and Q values In PCA scores plot option to display the Hotelling s TZ statistic e Usability enhancements Ability to export analysis steps as PDF reports merge reports with other reports and share reports in cloud storage Ability to merge compounds split in retention time domain while creating Unidentified or Combined Mass Profiler Professional experiments Ability to use the clipboard to export data from multiple pathways For heatstrips drawn on pathway views multiple colors to denote the experiment type Dendrogram view updated to respond dynamically to changes in the active entity list Ability to export images in SVG and EPS formats e MassHunter complementary features Ability to create Mass Profiler Professional experiments from CEF files that were generated with the Find by Integration algorithm MassHunter ID Browser B 07 00 MassHunter Profinder B 06 00 Service Pack 1 Mass Profiler Professional Quick Start Guide 3 Where to Find More Information Online help Press F1 To get more information about a pane window or dialog box place the cursor on the part of the pane window or dialog box of interest and press F1 Help Menu Clic
22. rom Sample Prep Through Data Analysis Metabolomics Road Show March 2011 Training Videos Training videos can be found on the Supplemental disc Training Courses Visit www chem agilent com to view a listing of training courses for MPP Mass Profiler Professional Quick Start Guide Getting Started Getting Started How do I get started This Quick Start Guide helps you launch MPP activate your license review the MPP user interface and create a project and an experiment that you import data into and then use to begin your analysis If you are already familiar with the MPP software after you install MPP you can immediately start using the preloaded demonstration project called Malaria Start and Explore Mass Profiler Professional 1 Double click the Mass Profiler Professional icon o located on your desktop or click Start gt All Programs gt Agilent gt MassHunter Workstation gt Mass Profiler Professional gt Mass Profiler Professional Activate your license The first time you start MPP you are prompted to enter your Mass Profiler Professional Order ID before you can use the software see Activating a License on page 7 Review the following three sections in this Quick Start Guide User Interface on page 10 Basic Tasks on page 15 Advanced Tasks on page 24 Review the Mass Profiler Professional Familiarization Guide p n G3835 90010 see Documents on page 4 This guide helps yo
23. s has been previously used to identify some of the compound features x Experiment description training data Enter a name analysis type experiment type and a desired workflow type Analysis will guide you through a statistical significance test and Fold change analysis Data Import will guide you through experiment creation only Class Prediction will guide you through the creation and testing of a prediction model using imported Experiment description training data Enter a name analysis type experiment type and a desired workflow type Analysis will guide you through a statistical significance test and fold change analysis Data Import will guide you through experiment creation only Class Prediction will guide you through the creation and testing of a prediction model using imported Experiment name Malaria demo Experiment name Neue Analysistype Expression Analysis type Mass Profiler Professional 000 n Experiment type Agilent Expression Two Color o n gt Experiment type Unidentified o sl workflow type Analysis Biological Significance O n workflow type Analysis Significance TestingandFoldChange xf Experiment notes Experiment notes Malaria LCMS ESI pH 7 Help Help Cancel Mass Profiler Professional Quick Start Guide Cancel Your new project is now set up You are immediately guided through the steps to import and organize your data followed
24. s from the Bioinformatics Research Group at SRI International used under license http www biocyc org Citation based on use of BioCyc databases or the Pathway Tools software If you use BioCyc databases or the Pathway Tools software in your research cite relevant publications as described on the BioCyc website http biocyc org publications shtml Citation based on use of KEGG Database KEGG is developed by Kanehisa Laboratories If you use the KEGG database in your research cite relevant publications as described on the KEGG website http www genome jp kegg kegg1 html Mass Profiler Professional Quick Start Guide This page intentionally left blank Mass Profiler Professional Quick Start Guide 25 www agilent com In this book The Agilent G3S35AA MassHunter Mass Profiler Professional Software Quick Start Guide presents the first steps to use the MassHunter Mass Profiler Professional Software Agilent Technologies Inc 2014 Revision A September 2014 G3835 90019 E Agilent Technologies
25. se the operations available in the Workflow Browser e Create new project allows you to import an experiment from an existing project into the new project c lypeMalaria Project inName See Set up anew project on d Type Import Experiment in page 15 for creating a new project Notes and a new experiment e Click OK ElcreateNewProject__ I I E New Project Details New Project Details Name New Project Name Malaria Project Notes Import Experiment ES Cancel l Mass Profiler Professional Quick Start Guide 21 Basic Tasks Steps Detailed Instructions Comments f Click Open existing experiment in the Experiment Selection Dialog dialog box experiment Selection Dialog i xj 4n experiment is an organized collection of LEMS or GCIMS sample data From a given data source IF you have an experiment you wish to use From a previous project please choose Open existing experiment You may also create a new experiment with new data or previously imported data Choose Experiment f Create new experiment g Select the Malaria LCMS ESI pH7 e The selected experiment is shown experiment in the Add Experiment highlighted using a background dialog box color h Click Add e The Malaria LEMS ESI pH 7 experiment in the Malaria project is now imported into your new project and appears as if it was opened using Open recent project e You can now use the operati
26. u quickly create a project create an experiment import and organize data and create an initial differential expression using pre installed demonstration data Malaria Demo Review the Mass Profiler Professional Application Guide p n G3835 90021 see Documents on page 4 This guide provides you with more detail about the MPP software and helps you create a project create an experiment import and organize data and create an initial differential expression with your own data Perform advanced analyses to meet your project needs using the operations available in the Workflow Browser see Workflow Browser on page 13 Mass Profiler Professional Quick Start Guide Getting Started License Management Activating a License The first time you start MPP you enter your Order ID License activation information is entered in the Mass Profiler Professional License Activation dialog box shown in Figure 1 An Internet network connection is required 1 Mark Mass Profiler Professional Order ID If you have additional software product licenses such as for Pathway Architect or GeneSpring mark your additional products 2 Enter your Mass Profiler Professional Order ID If you have additional software product licenses such as for Pathway Architect or GeneSpring enter your additional product Order IDs 3 Click OK The Mass Profiler Professional software automatically validates your license and starts Mass Profiler Professional
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