The Agilent

MassHunter Software

One Software for all Agilent Mass Spec

Systems

MassHunter – The most innovative MS SW !

MassHunter Workstation One software for all Agilent MS Systems

LC/MS GC/MS ICP-MS

Minimize learning (and maximize productivity)

with a common software for all of your

mass spec systems

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)

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

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

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

MassHunter Workstation Increase your productivity significantly

MassHunter

Optimizer

Optimize

Compounds

MassHunter

Acquisition

Acquire

Samples

MassHunter

Study

Manager

Submit Study

Excel or

other

Electronic

Source

Import Sample

Set

End User

App

Software

Calculate

Values Report

MassHunter

Quant

Reporting

MassHunter

Quant

Review

Results

MassHunter

Quant

Analyze Batch

Compound

Database

High-Throughput Targeted Quant in Drug Discovery

“In vitro” screening using Study Manager

Which of the synthesized compounds

will be viable drug candidates?

Study Manager schedules

and automates these steps

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

MassHunter B.06.00 Key Qualitative Applications

Accurate Mass LC-MS/MS Identification with 6500 QTOF

Accurate Mass LC/MS/MS Identification

Biopharmaceuticals

• Identification

• Characterization

• Accurate Mass LC/MS/MS Support

• MassHunter Comparative Analysis

Screening and ID Metabolomics

• 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

MassHunter Workstation B.06.00 for TOF/Q-TOF

Confident Screening + ID in Forensics, Food and Environment

• 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.

Sample (Blood, Urine, Extracts, …)

Find by Formula

Directed MS/MS

MH data file

Compound AM

MS/MS spectra

PCDL Search

Auto MS/MS

MH data file

Cmpds confirmed

via AM MS/MS

Print Report

Find by MFE +

MS/MS extraction

Compounds with

AM MS/MS spectra

PCD(L) Search

Cmpds identified

via AM MS+MS/MS

Identification of

true unknowns Report

MFG

Similarity

Search

Report

Print Report

MassHunter PCDL Manager B.04.00

Create/edit customized local 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!)

SUPPORTS:

METLIN AMRT PCD B.04.00

METLIN AMRT PCDL B.04.00

For/Tox AM PCD B.04.00

For/Tox AM PCDL B.04.00

Pesticide AM PCD B.04.00

The most

comprehensive

offering of

content PCDs

and PCDLs

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

Pesticides 1609 compounds N/A

Glycans 144 compounds N/A

Find biomarkers

for early disease

detection !

To analyze the

food you eat !

Crime Scene

Investigation !

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!

Agilent Differential Analysis Workflow

Metabolomics, Proteomics & Untargeted Screening G

CM

S

LC

MS

Separation

& Detection

GC/MSD

GC-QQQ

LC-TOF/QTOF

LC-QQQ

Find features

& Quantitate

MassHunter Qual AMDIS or Find by

chromatographic

deconvolution

MassHunter Qual MFE,

Find by Formula,

Find by Ion

Alignment

& Statistics

Mass Profiler Professional (MPP)

Identify

& Annotate

ID Browser

Pathway

Analysis

Pathway

Module

Mass Profiler (MP)

ID Browser

Multivariate

Analysis

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

Agilent Differential Analysis Workflow

Target applications

ASMS Metabolomics Bottleneck Summary

2009 ASMS Metabolomics Survey Results

http://metabolomics.us/2009/ASMSMetabolomicsWorkshop/SurveyResults/

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%

!!!

New METLIN AMRT PCD and PCDL B.04.00

MS/MS spectra for ~ 2300 endogenous metabolites !

• Now contains ~ 25000 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)

New MassHunter BioConfirm B.05.00

More confidence in identification of biopharmaceuticals

Higher confidence in peptide

identification using an accurate

mass MS/MS score

=> Reduce false positives

Allows to clearly identify sites of

modification, e.g.:

TSPYVLPVPFLNVLNGGSHAGG

ALALQEFMIAPTGAK

=> Unique ions confirm

Oxidation at Met

Adding the power of

accurate mass MS/MS !

New MassHunter Comparative Analysis B.05.00

Compare two protein samples and visualize the difference

Coloring whether

found in sample,

Reference, or both

Compare chromato-

grams (TIC, ECC,

BPC, TCC) via

mirror plot

Compare MS and

MS/MS spectra

underneath each

other

Visualize and

compare sequence

coverage in both

samples

Faster performance

and larger data sets

with native 64-bit

code

MassHunter Metabolite ID

Easy, confident and highly productive Metabolite ID

Page 19

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)

• 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.

Sample Control

Compounds Compounds

Potential Metabolites

Identified Metabolites

MFE MFE

Compare

Confirm + identify

MassHunter Metabolite ID

Easy, confident and highly productive Metabolite ID

THANK YOU!

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

MassHunter 64 – Integrated Software Tools

Quantify Identify

• Qualitative Analysis B.05.00

• BioConfirm B.05.00

• Molecular Structure Correlator (MSC) B.05.00

• Quantitative Analysis B.05.01

• MassHunter Acquisition for TOF/Q-TOF B.05.00

• MassHunter Acquisition for QQQ B.05.00

Confidence

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

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

Workstation)

Up to 24 GB optional Windows 7 Pro

--MassHunter Qual

--MassHunter Quant

MH Qual B.05.00 Identify MORE Compounds with Greater Confidence

• Metabolomics customers can perform Find-by-Formula on the entire METLIN database (24,768 entries) in minutes

Use large databases as a Formula Source

• Forensics customers with Q-TOFs can run in Auto MS/MS mode, then Find-by-Formula on Forensics/Tox (7360 compounds), and match their MS/MS spectra (available in B.05.00) against the Forensics/Tox PCDL

MS/MS Libraries searches on FbyF compounds

• Suspect targets in Find-by-Formula are flagged and can be manually reviewed

• Manually add missed compounds

Manual review and override are easy

Find-by-Formula is now 20x faster therefore replacing Molecular Feature Extractor as the tool of choice for targeted workflows

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

MassHunter 64 – Identify with Confidence

BioConfirm B.05.00 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

MassHunter 64 – Identify with Confidence

Molecular Structure Correlator (MSC) B.05.00

• 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

Proadifen MSC

MassHunter 64 – Quantify with Confidence

Quantitative Analysis B.05.01

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

MassHunter 64 – Identify and Quantify with

Confidence

MassHunter LC/MS Acquisition B.05.00

• 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

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

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

In Summary… MassHunter Programs Give You Confidence

Quantify Identify

• Qualitative Analysis

• BioConfirm

• Molecular Structure Correlator (MSC)

• Quantitative Analysis

• MassHunter Acquisition for TOF/Q-TOF and QQQ

Confidence