Workstation Software in mass spectometryWATSON LIMS •Call of Optimizer from Study Manager •Automatic Acq + Quant Method update Reporting. ... Module (New !) ID Browser (New !)

Page 1

Importance of Software in

Mass Spectrometry

Dec-7, 2009

Agilent MassHunter

Workstation

Importance of

Software in mass

spectometry

Frank Kuhlmann

Product Manager

LC/MS Software Solutions

Agilent Technologies

Agilent MS User Meeting

Würzburg Dec 7, 2009

Automation

Integrated workflows

Easy to learn and to use

One software for all instruments

Page 2


Mass Spectrometry

Dec-7, 2009

Software in the Analytical Workflow

Sample Prep Data AcquisitionData Processing

& ReportingSTEPS

TOTAL TIME

PEOPLES TIME

Fast method

developm.

Fast data acquisition

Intelligent data acquis.

SOFTWARE

Algorithms

Application SW

Efficient data review

Flexible reporting

Productivity (Cost per Sample)

ResultQuality

Accuracy

Confidence

Completeness

Relevance

HARDWARE

Sensitivity, Dyn. range

Mass Accuracy

Resolution (LC + MS)

Fast acquisition speed

Page 3


Mass Spectrometry

Dec-7, 2009

Software Challenges for MS Users

• Easy to learn

• Ease of use

– Simplified data entry

– Minimized repetitive tasks

• Stability

• Performance

• Automation

• Complete feature set for application

• Need one software for all instruments

We know that there is always room for Improvement and some things are painful !

Page 4


Mass Spectrometry

Dec-7, 2009

Software Challenges for Vendors

• Maintain good communication and listen to

the user (requirements)

• React quickly to new application needs

• React quickly to user requests

• Increase the domain knowledge of the software developers

• Find a balance between flexibility (options) and ease-of-use

• Provide a complete feature set for specific workflows

• Supporting more users, instruments and applications !

Did you know that in LC/MS, Agilent has moredevelopers working on software than hardware?

Page 5


Mass Spectrometry

Dec-7, 2009

MassHunter WorkstationOne software for all Agilent Mass Spectrometers

• Control of Agilent 6000 Series QQQ, TOF and Q-TOF

• Control of most 1100 and 1200 Series HPLC modules incl. Chip-LCMS

• LC/MS Data Processing from QQQ, TOF, Q-TOF and SQ

• Control of GC/MS/MS & data processing for GC/MS and GC/MS/MS

• Control & data processing for ICP/MS

• FUTURE: Control of LC/SQ and GC/SQ, processing of LC/Trap data

LC/MS GC/MS ICP-MS

Did you know that all Agilent software developers on MassHunter are very passionate about developing the best product on the market ?

Page 6


Mass Spectrometry

Dec-7, 2009

Importance of Software in Data Acquisition

Firmware Quant data processingData acquisition Qual data processing

• Firmware is low-level software code which mediates between hardware

and acquisition software.

• Firmware e.g. deals with 4GHz digitization, 10kHz transient rate,

acquisition rate > 20 spectra/s, and manage dual channel amplification

in the extended dynamic range mode, unique to Agilent’s TOF and Q-

TOF technology.

• Data-dependent Auto MS/MS (Q-TOF)

and Dynamic MRM mode (QQQ) is

calculated in the firmware.

• Firmware takes care of filtering

and compression of spectra.

Reporting

http://www.clker.com/clipart-11120.html

Page 7


Mass Spectrometry

Dec-7, 2009

Importance of Software in Data acquisition


Intelligent acquisition of MS/MS data

• QQQ: Acquisition of as many MRM transitions per run as possible at

maximum dwell time for complex samples => Dynamic MRM allows to

acquire up to 4000 transitions in one run (1000 compounds @ 4

transitions).

• Q-TOF: Data dependant MS/MS acquisition of as many untargeted

compounds of interest as possible in complex sampes.

– Improvements in the DDE engine, e.g. better timing on when to

take spectra and triggering based on mass-defect filter.

• Q-TOF: Targeted MS/MS acquisition for highest quality spectra of many

compounds of interest. Similar to Dynamic MRM.

Reporting

Ultra High Definition – Complex Targeted Analysis~ 40 Pesticides Eluting in a 1 minute RT Window

10.5 10.6 10.7 10.8 10.9 11.0 11.1 11.2 11.3 11.4 11.5 min

1.00

0.75

0.50

0.25

0.00

Associate MRM Transitions with each CompoundA 30 sec window at 11.0 min has 20 Compounds

1:40 Duty Cycle25 msec Dwell/sec

15 sec 15 sec

ConcurrentCompounds

Dynamic MRM Simulation

Time >>>

Ab

un

dan

ce >

>>

Page 10


Mass Spectrometry

Dec-7, 2009



• DMRM Viewer

• Change Static to DMRM

Method, update RTs

• Split DMRM method

Reporting

MassHunter QQQ Acquisition B.03.01 (early-2010)

Page 11


Mass Spectrometry

Dec-7, 2009



MassHunter QQQ Acquisition B.03.01 (early-2010)

• Support of ADME/PK

workflows in Pharma

• NEW: MassHunter

Study Manager

• Integration with

WATSON LIMS

• Call of Optimizer from

Study Manager

• Automatic Acq + Quant

Method update

Reporting

Page 12


Mass Spectrometry

Dec-7, 2009

Importance of SW in Quant data processing


MassHunter Quantitative Analysis B.04.00 (early-2010)

• Simplify data review for a

large number of compounds

=> Compounds-at-a-glance

• Improved 2nd generation

parameter-less integrator

• Improve reporting performance

and increase template options

• Add first set of cross batch

trend reporting capabilities.

• Review multiple batches in

ADME/PK studies

• Support Dynamic MRM GC/MS

Reporting

Page 13


Mass Spectrometry

Dec-7, 2009

Importance of SW in Qual data processing


MassHunter Qualitative Analysis B.04.00 (mid-2010)

• Improved algorithms: 2nd gen parameter-less integrator,

Find-By-MRM for easier input of MRM data into MPP,

support of 6540 high-res spectra.

• NEW: “Compare analysis” mode to compare two samples

Find-by-MFE in two samples, then parallel visualization of compound

mass spectra and chromatograms.

• Combined Find-by-MFE and Find by Auto MS/MS to generate follow

up acquisitions via Targeted MS/MS.

• Annotation of text and graphics to spectra and chromatograms.

• Delta-mass caliper for automatic annotation of accurate mass deltas

• Performance improvements on MFE and EIC extraction.

Reporting

Page 14


Mass Spectrometry

Dec-7, 2009

Importance of Software in Reporting

Firmware Quant data processingData acquisition Qual data processing Reporting

Reporting improvements

• Speed improvement of Quant reports x 3

• More report templates

• Direct plot reports from Qual without Excel

• Increased capacity to assist customers in custom report generation

• NEW: interactive Video Tutorial for Excel custom reporting now shipping!

• NEW: first set of cross batch trend reporting capabilities in MassHunter

Quant via Excel Pivot Tables.

Page 15


Mass Spectrometry

Dec-7, 2009

Importance of SW in enabling Workflows

• Mass Profiling Workflow

for Differential Analysis

• Screening and ID of Targeted

Compounds and Unknowns

Some applications require integration of several software

modules and easy results transfer from one step to the next !

Page 16

Mass Profiling Workflow for Differential Analysis

Metabolomics + Proteomics

• Biomarker Discovery

• Together with Genomics in Systems Biology (GeneSpring platform)

• Environmental Metabolomics

• Plant Metabolomics to create more resistant species

General mass spec based differential analysis

• Food, beverages, flavors and fragrances

– Adulteration and fraud (natural products)

– Origin determination and authenticity

– ID of compounds and degradends affecting taste, texture, smell

• Degradation Studies

• Optimization of complex manufacturing processes of products

• Follow blood metabolome of athletes over time

• Compare water from different wells, locations in a river

Page 17

31-May-2009

Mass Profiler Professional

Update

ASMS 2009 Field Training

The Advanced Agilent Metabolomics WorkflowG

CM

SL

CM

S

separate

+ detect

find features

+ quantitate

identifystatistics pathways

Mass

Profiler Pro

(New !)Qual- MFE

- FbF

- FbI (New!)

Qual- AMDIS

- FbCD

LC/TOF

LC/Q-TOF

LC/QQQ

GC/MSD

GC/QQQ

Pathway

Analysis

Module

(New !)

ID Browser

(New !)

Recursive2nd pass extraction with Find-by-Ion

(New!)

Quant

Unified Compound Exchange File (.cef) (New !)

Page 18


Mass Spectrometry

Dec-7, 2009

Mass Profiler Professional B.02.00New UI and architecture - Guided Workflow

2) Follow

steps in

workflow

wizard

3) Get

explanation

for each step

in workflow

1) Select

preconfigured

workflow

=> More powerful than GeneSpring MS 1.2.1, but much easier to use !

Page 19


Mass Spectrometry

Dec-7, 2009

Mass Profiler Professional B.02.00NEW optional integrated Pathway Analysis software

=> Once markers are ID’d, determine the biological context!

Agilent is only MS vendor with integrated PA software!

Page 20

ASMS Workshop Unknown

Analysis with Hi Res Mass

SpecJun-3, 2009

TOF/Q-TOF Screening and Unknowns Analysis

• Combination of UHPLC separation and accurate mass TOF technology

• Effective data mining algorithms to easily FIND compounds in a sample

• Optional SW to easily COMPARE samples or sample sets to identify

differences

• AMRT DBs and MS/MS Lib Search to easily IDENTIFY targeted

compounds

• Several algorithms to IDENTIFY unknown compounds (MFG, MSC)

• User Interface to easily NAVIGATE RESULTS

• Custom reporting to comprehensively REPORT results

• Full AUTOMATION of data acquisition, processing and reporting

TOF/

Q-TOF

Analysis

ID via

AMRT

DBs

Molecular

Feature

Finding

MFG of

Unknowns

w/ MSMS

MSMS

structural

correlation

ID via

MSMS

libraries

OPTION:

Differential

Analysis

Print

custom

report

Automation

Page 21



SpecJun-3, 2009


TOF/

Q-TOF

Analysis

Molecular

Feature

Finding

MSMS

structural

correlation

Automation

OPTION:

Differential

Analysis

Molecular Feature Extractor (MFE)

• Works on the 3-dimensional data set

• Remove noise

• Group covariant mass signals

• Combine signals with chemical relations

• Create extracted compound chromatograms & spectra

Print

custom

report

ID via

AMRT

DBs

MFG of

Unknowns

w/ MSMS

ID via

MSMS

libraries

=> It’s crucial to find all

detectable compounds

in a sample efficiently

Page 22



SpecJun-3, 2009


TOF/

Q-TOF

Analysis

ID via

AMRT

DBs

Molecular

Feature

Finding

MFG of

Unknowns

w/ MSMS

MSMS

structural

correlation

ID via

MSMS

libraries

Automation

OPTION:

Differential

Analysis

Identification of targeted compounds via AM or AMRT databases

• Personal Compound Databases (PCD)

• PCD for forensics and toxicology with 7000 compounds

• PCD with 1600 pesticides from 5 regional regulatory labs Europe/Asia

• The addition of retention time into the database search (AMRT) enables

unambigous identification of isobaric compounds

Print

custom

report

Page 23 Jun-3, 2009


TOF/

Q-TOF

Analysis

ID via

AMRT

DBs

Molecular

Feature

Finding

MFG of

Unknowns

w/ MSMS

MSMS

structural

correlation

ID via

MSMS

libraries

Automation

OPTION:

Differential

Analysis

LC/MS/MS library search

• NIST LC/MS/MS library

• Agilent PCDL libraries

• Support of multiple CEs

• Content MS/MS libraries

in development:

• Forensics/Tox

• Endogenous Metabolites

• Glycans

Print

custom

report

Page 24



SpecJun-3, 2009


TOF/

Q-TOF

Analysis

ID via

AMRT

DBs

Molecular

Feature

Finding

MFG of

Unknowns

w/ MSMS

MSMS

structural

correlation

ID via

MSMS

libraries

Automation

OPTION:

Differential

Analysis

Molecular Formula Generation of Unknowns

• MS level scoring based on isotope mass, isotope spacing AND abundance

• Exploit MS/MS fragment ion and neutral loss information

Print

custom

report

Monoisotopic mass(varies in ppm)

Isotope spacing(varies in ppm)

Isotope distribution(varies in %)

Page 25



SpecJun-3, 2009


TOF/

Q-TOF

Analysis

ID via

AMRT

DBs

Molecular

Feature

Finding

MFG of

Unknowns

w/ MSMS

MSMS

structural

correlation

ID via

MSMS

libraries

Automation

OPTION:

Differential

Analysis

MS/MS Structural Correlation (MSC) = > FUTURE

Print

custom

report

• Algorithm to correlate

“proposed structures” with

accurate mass MS/MS

fragment ion spectrum.

• Favor systematic bond

dissociation approach over

rule based fragmentation

prediction approach.

Workstation Software in mass spectometryWATSON LIMS •Call of Optimizer from Study Manager •Automatic Acq + Quant Method update Reporting. ... Module (New !) ID Browser (New !)

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