guided omics discovery with the latest progenesis qi software · metascope, for searching your own...
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©2014 Waters Corporation 1
Guided Omics discovery with the
latest Progenesis QI software
Waters MS Technology Days 5th and 6th November 2014
Martin Wells
©2014 Waters Corporation 2
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
©2014 Waters Corporation 3
Two versions of software
Quantify
Identify
For ‘large molecules’
Proteomics
Biomarkers
Food allergens
Etc
©2014 Waters Corporation 4
Two versions of software
Quantify
Identify
For ‘small molecules’
Wide applicability
Metabolomics
Biomarkers
Food
Wine
Toxicology
Environmental
Pesticides
Etc
©2014 Waters Corporation 5
Progenesis QI
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100
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200
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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.
©2014 Waters Corporation 6
Software ‘Difference Engines’
Detect Quantify Compare Identify
‘Another age must be the judge’
©2014 Waters Corporation 7
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
©2014 Waters Corporation 8
‘Typical’ biomarker workflow
Reduce no. analytes; reduce analysis time/sample
Rodriguez H. Prot. Clin. App. (2010);4:904-14 NCI-CPTC Group
©2014 Waters Corporation 9
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
©2014 Waters Corporation 10
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
©2014 Waters Corporation 11
Progenesis QI for proteomics
©2014 Waters Corporation 12
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
©2014 Waters Corporation 13
Data Import Multi-vendor support
©2014 Waters Corporation 14
Workflow Automation
©2014 Waters Corporation 15
Review alignment (zoom) Un-aligned
©2014 Waters Corporation 16
Review alignment (zoom) Aligned
©2014 Waters Corporation 17
Peak picking and Co-detection
Aggregate co-detection
Mapping the peak picking to all runs avoids missing data
©2014 Waters Corporation 18
Consistent measures across all files
Spiked data run in triplicate
©2014 Waters Corporation 19
Progenesis Co-Detection
©2014 Waters Corporation 20
Quantify co-eluting peptides
©2014 Waters Corporation 21
Experiment Design
Multiple Experiment Setups can be created before and after Peak Picking
©2014 Waters Corporation 22
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.
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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.
©2014 Waters Corporation 24
Statistics - PCA
Explore the full identified Protein set for differential analysis using multivariate statistics. Look for differential behaviour based on clustering of samples
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Proteins Identified
©2014 Waters Corporation 26
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.
©2014 Waters Corporation 27
QC-Metrics
©2014 Waters Corporation 28
QC-Metrics
©2014 Waters Corporation 29
Congratulations! You found the differences
Rapidly
Objectively
Reliably
©2014 Waters Corporation 30
Progenesis QI A significant new product for small molecules
©2014 Waters Corporation 31
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
©2014 Waters Corporation 32
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)
©2014 Waters Corporation 33
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
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Automatic reference sample selection/alignment
©2014 Waters Corporation 35
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
©2014 Waters Corporation 36
Review adduct deconvolution
Deconvolution is automatically performed during Peak Detection
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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
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Theoretical fragmentation search result
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Fragment database search result Mirror plot
©2014 Waters Corporation 40
Make your own fragment DB with export function
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Integrated Statistics with optional export to EZinfo
Export data to EZInfo and explore
©2014 Waters Corporation 42
Extended Statistics Package “Ezinfo” from Umetrics
©2014 Waters Corporation 43
Review Compounds
©2014 Waters Corporation 44
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
©2014 Waters Corporation 45
"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