guided omics discovery with the latest progenesis qi software · metascope, for searching your own...

©2014 Waters Corporation 1

Guided Omics discovery with the

latest Progenesis QI software

Waters MS Technology Days 5th and 6th November 2014

Martin Wells


The next generation of OMICS data analysis software

Rebrand following Waters acquisition of NLD in 2013

Enhance and streamline product offerings

Focuses resources to deliver world-leading informatics platform

Maintain support for multi-vendor LC-MS data


Two versions of software

Quantify

Identify

For ‘large molecules’

Proteomics

Biomarkers

Food allergens

Etc


Two versions of software

Quantify

Identify

For ‘small molecules’

Wide applicability

Metabolomics

Biomarkers

Food

Wine

Toxicology

Environmental

Pesticides

Etc


Progenesis QI

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50

100

150

200

250

300

2009 2010 2011 2012 2013 2014

Progenesis publications.

With >450 licenses installed to date and growing fast. Progenesis continues to be the software of choice for many research institutes. Visit www.nonlinear.com to view the publications by title and author and read the numerous customer endorsements.

http://www.nonlinear.com/


Software ‘Difference Engines’

Detect Quantify Compare Identify

‘Another age must be the judge’


What do we do with the software? Relative quantification (mostly)

To discover the proteins/compounds that warrant

further investigation as rapidly, objectively and

reliably as possible

Mean ± Variance

Control Test


‘Typical’ biomarker workflow

Reduce no. analytes; reduce analysis time/sample

Rodriguez H. Prot. Clin. App. (2010);4:904-14 NCI-CPTC Group


Informatics will be critical

“ While the last 10 years of MS-based proteomics were driven by

improvements in MS-hardware performance, it is my feeling that

the next 10 years will be driven by informatics.”

Professor Bernhard Kuster, Technische Universitaet Muenchen


Progenesis QI Similar workflows / easy to learn

Alignment

Peak Detection

Identification

Protein

Quantitation

Statistics

Meta

bo

lom

ics/

Lip

idom

ics

Pro

teo

mic

s

Peptide

Quantitation

Alignment

Peak Detection

Compound

Quantification

Identification

Statistics

Deconvolution


Progenesis QI for proteomics


Consistent peak picking across all runs, vital for accurate and precise quantification

No restrictions on the number of groups, samples or experimental designs you can compare within your analysis

Complete data matrix and no missing values, for reliable multivariate statistics

Query databases using common search engines

Fully compatible with ion mobility to achieve three dimensions of resolution

Powerful data visualization and guided-workflow for DIA and DDA analyses as well as support for analysis of fractionated samples

Progenesis QI for proteomics Key Product Attributes


Data Import Multi-vendor support


Workflow Automation


Review alignment (zoom) Un-aligned


Review alignment (zoom) Aligned


Peak picking and Co-detection

Aggregate co-detection

Mapping the peak picking to all runs avoids missing data


Consistent measures across all files

Spiked data run in triplicate


Progenesis Co-Detection


Quantify co-eluting peptides


Experiment Design

Multiple Experiment Setups can be created before and after Peak Picking


Protein Identification / Database Search

Optional search algorithms

MSE and HDMSE with PLGS

– (‘MSE Search’)

DDA and HD-DDA with Mascot, or any

other search engine of choice.


Protein Quantification

Any peptide ions with “conflicting” identifications are automatically excluded from the protein quantification. Proteins with entirely common sequence coverage will be automatically grouped. Absolute Quantification using HiN approach can be applied.


Statistics - PCA

Explore the full identified Protein set for differential analysis using multivariate statistics. Look for differential behaviour based on clustering of samples


Proteins Identified


Data Interpretation – Pathway Analysis

New in Progenesis QI v2 you have the convenient options to export all data for more comprehensive biological interpretation. This can be interface to a variety of commercial and academic pathway tools.


QC-Metrics


Congratulations! You found the differences

Rapidly

Objectively

Reliably


Progenesis QI A significant new product for small molecules


Progenesis QI - Key product attributes

Consistent peak picking for accurate and precise quantification

Metascope, for searching your own and/or third-party databases

Compound ID using exact mass, MS/MS fragments, isotope

distribution, RT and CCS

No Missing Values for reliable multivariate statistics

Comprehensive data export options allow results to be combined with

other informatics data streams & create Publication Quality Reports

Powerful data visualization for DIA and DDA analyses with large

numbers of samples in one package


Progenesis QI

Fragment Ion Enabled ID

– e.g. High Energy MSE or DDA spectra

CCS Mediated Metabolite/lipid ID

Dimer/Trimer (adduct)

Deconvolution

Automated data import

– reference selection/alignment (options)


Progenesis QI guided workflow and data import / adduct selection

Details of data file format and a list of ‘expected’ adducts are entered to facilitate the handling of data import


Automatic reference sample selection/alignment


Similar actions as Progenesis QI for proteomics

Quantification

Alignment

Experiment design

Peak picking with co-detection

Intensity normalisation

Multivariate Statistical review and analysis

Identification

MetaScope Search Engine

Data review and Pathway Analysis


Review adduct deconvolution

Deconvolution is automatically performed during Peak Detection


Compound identification MetaScope search engine.

Compounds are identified using the integral MetaScope search engine and a compound database in Structure Data File (SDF)

NE

More search parameters for increased ID specificity

– Fragment ion data (.msp), CCS and Retention Time


Theoretical fragmentation search result


Fragment database search result Mirror plot


Make your own fragment DB with export function


Integrated Statistics with optional export to EZinfo

Export data to EZInfo and explore


Extended Statistics Package “Ezinfo” from Umetrics


Review Compounds


Conclusion

The next generation of OMICS data analysis software

Rapidly, objectively and reliably discover the significantly changing compounds

in your samples

Highly intuitive, easy to learn, workflow-guided software

Powerful data visualisation

Multi-vendor support for LC-MS data

Full user documentation and professional support by experienced scientists


"Thanks to its accurate alignment algorithm, its statistical tools, its simplicity of use and the easy to understand data reports, Progenesis QI for proteomics has been fully integrated in our label-free proteomic workflows.

Jean-Charles Sanchez and Alexandre Hainard Proteomics Core Facility,Centre Medical Universitaire (CMU) Genève, Switzerland

guided omics discovery with the latest progenesis qi software · metascope, for searching your own...

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