The Agilent MassHunter Software. One Software for all Agilent Mass Spec Systems

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1 The Agilent MassHunter Software One Software for all Agilent Mass Spec Systems

2 MassHunter The most innovative MS SW!

3 MassHunter Workstation One software for all Agilent MS Systems Minimize learning (and maximize productivity) with a common software for all of your mass spec systems LC/MS GC/MS ICP-MS

4 MassHunter Workstation Target Workflows and Key Software Tools Quantitative Applications (QQQ, TOF and QTOF) Targeted Quant in Food, Forensics/Tox, Environment (dmrm, tmrm, Quant) Proteomics Targeted Quant of proteins via peptide MRM (Skyline, dmrm, tmrm) Pharma Early ADME/DMPK (Study Manager, Optimizer) Bioanalysis and BA/BE (Study Manager, WATSON, 21CFRPart11) Qualitative Applications (TOF and Q-TOF) Metabolomics (Qual, MPP, ID via MFG, PCD, PCDL, Pathway Analysis) Characterization of Biopharmaceuticals (BioConfirm, Comparative Analysis) Screening + ID in Food, Forensics/Tox, Environment (Qual, PCD and PCDLs) Impurity and Degradant Analysis (MPP, MFG, PCD, PCDL) Pharma Compound Confirmation (Easy Access, Qual, ASR with TOF) Protein ID, PTM Analysis (Spectrum Mill with Q-TOF) Metabolite ID (Metabolite ID with Q-TOF)

5 MassHunter Workstation Increase your productivity significantly High Throughput Quantitation Study Manager to queue up quantitative assays incl. MRM optimization Optimizer quickly and easily optimizes MS/MS signal Dynamic MRM methods deliver robust assays faster WATSON LIMS Integration and Compliance support for BioAnalysis High Throughput Screening and Identification Personal Compound Databases (PCDs) and Libraries (PCDLs) for accurate mass DB and MS/MS library search with optional RT Fully automated acquisition, data processing and reporting Supports targeted and untargeted screening PCDL Manager software to view and edit PCDs and PCDLs Proteomics / Metabolomics & Non-targeted Screening Mass Profiler Professional (MPP) Integrated workflow for feature finding, alignment, differential analysis, identification and pathway analysis Powerful and easy-to-use statistical tools Pathway Analysis for direct biochemical pathway interrogation

6 High-Throughput Targeted Quant in Drug Discovery In vitro screening using Study Manager Import Sample Set Submit Study Optimize Compounds Acquire Samples Analyze Batch Review Results Report Calculate Values Excel or other Electronic Source MassHunter Study Manager MassHunter Optimizer MassHunter Acquisition MassHunter Quant MassHunter Quant MassHunter Quant Reporting End User App Software Compound Database Study Manager schedules and automates these steps Which of the synthesized compounds will be viable drug candidates?

7 Study Manager and Study Creators Queue up multiple assays for highest productivity User imports compound and worklist information via spreadsheets Study Manager creates worklists, schedules tasks for automated method development, acquisition, quantitation and reporting Different Study Creators for different workflows available

8 MassHunter B Key Qualitative Applications Accurate Mass LC-MS/MS Identification with 6500 QTOF Biopharmaceuticals Screening and ID Metabolomics Identification Characterization Accurate Mass LC/MS/MS Support MassHunter Comparative Analysis Forensics/Tox Food Safety Environmental Accurate Mass MS/MS Library Broecker, Herre & Pragst Forensics/Tox PCDL Identification of Biomarkers METLIN AMRT PCD METLIN AMRT PCDL Accurate Mass MS/MS Library Accurate Mass LC/MS/MS Identification

9 MassHunter Workstation B for TOF/Q-TOF Confident Screening + ID in Forensics, Food and Environment Sample (Blood, Urine, Extracts, ) Directed MS/MS MH data file Find by Formula Compound AM MS/MS spectra PCDL Search Cmpds confirmed via AM MS/MS Print Report Report Auto MS/MS MH data file Find by MFE + MS/MS extraction Compounds with AM MS/MS spectra PCD(L) Search Cmpds identified via AM MS+MS/MS MFG Similarity Search Identification of true unknowns Print Report Targeted Workflow Highest productivity via automatic Finding, identifying and confirming targeted compounds via Find by Formula using accurate mass MS info Easily create a Personal Compound Database and Library (PCDL) from targeted compounds via PCDL Manager Confirm identity via accurate mass MS/MS spectra library search in a PCDL via new Directed MS/MS in the first run! Untargeted Workflow Highest productivity via automatic extraction of accurate mass MS and MS/MS info via Find by MFE with MS/MS spectral extraction from Auto MS/MS data files. Automatically conduct a PCDL search and Molecular Formula Generation using MS and (!) MS/MS information Highest confidence via combined scoring and viewing of results from AM DB search, AM library search and MFG. Report

10 MassHunter PCDL Manager B Create/edit customized local PCDs and PCDLs SUPPORTS: METLIN AMRT PCD B METLIN AMRT PCDL B For/Tox AM PCD B For/Tox AM PCDL B Pesticide AM PCD B The most comprehensive offering of content PCDs and PCDLs Personal Compound Database and Libraries (PCDLs) for accurate mass database and MS/MS library search with optional retention time Add compounds, AM MS info, RT info and AM MS/MS spectra at multiple collision energies using the new PCDL Manager software Use create and edit PCDs and PCDLs on your personal PC (keep proprietary data in house!)

11 LC/MS Database and Library Products Personal Compound Databases (PCDs) for use with accurate mass data; Personal Compound Database and Libraries (PCDLs) adds ability to library search MS/MS spectra Application PCD PCDL Metabolomics METLIN (24,768 compounds). METLIN (adds spectra for 2286 compounds) Forensics / Tox 7360 compounds Adds spectra for 2720 compounds Crime Scene Investigation! Pesticides 1609 compounds N/A Glycans 144 compounds N/A Find biomarkers for early disease detection! To analyze the food you eat!

12 Forensics/Tox Accurate Mass PCDL Broecker, Herre & Pragst MS/MS spectra for 2720 Cmpds Extract MS/MS Spectra when running MFE Identification via accurate mass MS/MS Lib Search The Forensics/Tox accurate mass PCD contains 7360 compounds Forensics/Tox accurate mass PCDL contains 8263 MS/MS spectra for over 2720 compounds from 3 collision energies mostly in positive mode. => The first (!) commercially available accurate mass MS/MS library!

13 LCMS GCMS Agilent Differential Analysis Workflow Metabolomics, Proteomics & Untargeted Screening Separation & Detection Find features & Quantitate Alignment & Statistics Identify & Annotate Pathway Analysis Mass Profiler (MP) ID Browser GC/MSD GC-QQQ MassHunter Qual AMDIS or Find by chromatographic deconvolution Mass Profiler Professional (MPP) Multivariate Analysis ID Browser Pathway Module LC-TOF/QTOF LC-QQQ MassHunter Qual MFE, Find by Formula, Find by Ion

14 Agilent Differential Analysis Workflow Target applications Life Sciences Basic Research (Academic) - Improve understanding of biological processes Clinical Research - Improve understanding and treatment of human diseases Pharmaceutical Identify toxicological problems, develop efficacy biomarkers Chemical analysis Agriculture - Increase crop efficiency (yield, drought and pest resistance, nutritional value) Nutrition Analysis of food quality, alteration, origin, nutritional value) Environmental - Understand effect of pollution on environment

15 ASMS Metabolomics Bottleneck Summary 81% of respondents say challenges due to software NOT hardware 1. Compound Identification 35% 2. Biological Significance 27% 3. Data Processing 14% 4. Statistical Analysis 5%!!! 2009 ASMS Metabolomics Survey Results

16 New METLIN AMRT PCD and PCDL B MS/MS spectra for ~ 2300 endogenous metabolites! Now contains ~ endogenous metabolites METLIN AMRT PCD added retention times for 670 compounds on a RP column. Additional RTs on a hydrophilic column in progress. METLIN AMRT PCDL contains MS/MS spectra from over 2286 compounds from up to 3 collision energies in positive and/or negative mode (~ 9000 spectra total)

17 New MassHunter BioConfirm B More confidence in identification of biopharmaceuticals Higher confidence in peptide identification using an accurate mass MS/MS score => Reduce false positives Adding the power of accurate mass MS/MS! Allows to clearly identify sites of modification, e.g.: TSPYVLPVPFLNVLNGGSHAGG ALALQEFMIAPTGAK => Unique ions confirm Oxidation at Met

18 New MassHunter Comparative Analysis B Compare two protein samples and visualize the difference Faster performance and larger data sets with native 64-bit code Coloring whether found in sample, Reference, or both Compare chromatograms (TIC, ECC, BPC, TCC) via mirror plot Compare MS and MS/MS spectra underneath each other Visualize and compare sequence coverage in both samples

19 MassHunter Metabolite ID Easy, confident and highly productive Metabolite ID Productivity One-click Metabolite ID data processing Compound-centric data navigation Summary view of results at a glance Comprehensive Comparison of sample and control via untargeted approach based on Molecular Feature Extraction (MFE) Predicted and unexpected metabolites Confidence in Results Widest range of and most sophisticated algorithms (MFE, MFG, Novatia Autoshift) Page 19

20 MassHunter Metabolite ID Easy, confident and highly productive Metabolite ID Sample Control MFE MFE Compounds Compounds Compare Potential Metabolites Confirm + identify Identified Metabolites Productivity and Confidence Sophisticated Sample-Control Comparison Algorithm based on Molecular Feature Extraction (MFE) allows more comprehensive detection of differences via exploitation of accurate mass and RT. First find all differences in an untargeted approach and THEN confirm and identify Best suited to find and confirm expected and unexpected metabolites More confidence for confirming expected and identifying unexpected metabolites using multiple algorithms Novatia Autoshift algorithm to help located modifications via MS/MS spectral correlation.

21 THANK YOU!

22 Introducing MassHunter 64 Next Generation Platform More available memory to allow rapid processing of large data sets and multiple compound analyses Leveraging the enhanced speed of 64-bit processing for faster performance

23 MassHunter 64 Integrated Software Tools Quantify Confidence Identify Qualitative Analysis B BioConfirm B Molecular Structure Correlator (MSC) B Quantitative Analysis B MassHunter Acquisition for TOF/Q-TOF B MassHunter Acquisition for QQQ B.05.00

24 MassHunter 64 Improved Data Processing Limitations of 32-bit operating systems and applications 32-bit operating systems and programs can address a MAXIMUM of 4 GB of Random Access Memory (RAM) The Windows XP operating system (32-bit) is allocated 2 GB; all other programs are allocated up to 2 GB shared among them the result is slower performance and memory crashes 2 GB 2 GB Windows XP --MassHunter Qual --PCDL Manager --Anti-virus software

25 MassHunter 64 Harness the Power of 64-bit Improved performance for the most complex data sets: Windows 7 64-bit and native 64-bit applications can utilize up to 192 GB of RAM When a native 64-bit program such as MassHunter Qual runs on Windows 7, it can use all the remaining memory 2 GB 6 GB (shipping Windows 7 Pro Workstation) Up to 24 GB optional --MassHunter Qual --MassHunter Quant

26 MH Qual B Identify MORE Compounds with Greater Confidence Use large databases as a Formula Source Metabolomics customers can perform Find-by-Formula on the entire METLIN database (24,768 entries) in minutes MS/MS Libraries searches on FbyF compounds Forensics customers with Q-TOFs can run in Auto MS/MS mode, then Findby-Formula on Forensics/Tox (7360 compounds), and match their MS/MS spectra (available in B.05.00) against the Forensics/Tox PCDL Manual review and override are easy Suspect targets in Find-by-Formula are flagged and can be manually reviewed Manually add missed compounds Find-by-Formula is now 20x faster therefore replacing Molecular Feature Extractor as the tool of choice for targeted workflows

27 MassHunter 64 Identify with Confidence Personal Compound Database and Library (PCDL) Agilent is the first vendor to sell accurate mass MS/MS libraries Higher confidence identifications Run library searches from Qual or PCDL Manager Display structures and difference spectra of hits in Qual Customers can create their own libraries or append to a purchased library

28 MassHunter 64 Identify with Confidence BioConfirm B for more confident biopharmaceutical characterization Detect differences between even the most complex digests in less time (4000 peptides in 4 minutes) Peaks containing proteins with large differences in molecular weights can be deconvoluted successfully MS/MS support to confirm the location of PTMs

29 MassHunter 64 Identify with Confidence Molecular Structure Correlator (MSC) B Use MS/MS spectra to go from formula to structures Match substructures to specific fragments for positive identifications Access formula and structures from Agilent PCD/PCDLs or the ChemSpider database (26 million compounds) to provide the most likely structures (only Agilent offers this capability!) C23H31NO2 MSC Proadifen

30 MassHunter 64 Quantify with Confidence Quantitative Analysis B for the next generation of processing speed 5x Faster Accurate Mass Quantitation Easier Accurate Mass Method-building via import from Qual results Using Qual Find-by-Formula algorithm for more confident compound confirmation More confident confirmation of MRM data by comparing triggered MRM data to reference library

31 MassHunter 64 Identify and Quantify with Confidence MassHunter LC/MS Acquisition B Improved workflows New Study Creator for automatically importing worklists into the Study Queue Improved user interface for better usability Ability to quantify a peak and generate a report at the end of every run get your results back sooner than batch processing mode

32 MassHunter 64 Identify and Quantify with Confidence More confident compliance Improved log file tracks owner of each injection Audit trail on all Acquisition method changes New Audit Trail report for Quant results Easy connection to OpenLab ECM for secure data archival and retrieval

33 MassHunter 64 How to Upgrade 1. G3337AA MassHunter Workstation for QQQ Software Upgrade 2. G3849AA MassHunter Workstation for TOF/Q-TOF Software Upgrade 3. G3338AA MassHunter Workstation Offline Software Upgrade 4. G3336AA MassHunter Workstation Software Offline for customers who have an instrument and just want the offline software 5. G1668AA Windows 7 MassHunter Workstation HP Z400 with 8 GB RAM

34 In Summary MassHunter Programs Give You Confidence Quantify Confidence Identify Qualitative Analysis BioConfirm Molecular Structure Correlator (MSC) Quantitative Analysis MassHunter Acquisition for TOF/Q-TOF and QQQ

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