1. CPAS Comparative Proteomics Analysis System Adam Rauch LabKey Software adam@labkey.com

2. What Is CPAS? A proteomics analysis system that handles all data processing & management for high-throughput labs and core facilities

3. High-Throughput Proteomics Demands Integrate a wide variety of hardware & software – Instruments – MS/MS search engines – Quantitation, validation, and other analytic tools – Custom analysis tools – Computing hardware, operating systems, databases – IT infrastructure

4. High-Throughput Proteomics Demands Integrate a wide variety of hardware & software Rapidly analyze many large MS/MS runs – Search, validate, quantify, store millions of peptides per day – Re-analyze results, combine runs, experiment “in silico” – Automation and repeatability – Data analysis should not be the bottleneck

5. High-Throughput Proteomics Demands Integrate a wide variety of hardware & software Rapidly analyze many large MS/MS runs Manage huge volume of data – Organized and easily accessible results – Analysis & experimental protocols, sample information – Ability to answer biologically interesting questions: Compare runs & experiments to identify proteins of interest Search experiments specific proteins Query results linked to sample & experimental properties, rich protein annotations, custom protein annotation lists

6. High-Throughput Proteomics Demands Integrate a wide variety of hardware & software Rapidly analyze many large MS/MS runs Manage huge volume of data Collaborate easily while keeping data secure – Colleagues at same institution – Cross-institution collaborations and consortia – Publish results publicly – Appropriate and strong security

7. How CPAS Addresses These Demands Integrate a wide variety of hardware & software – CPAS is an integration platform – Integrates with SEQUEST, Mascot, and X! Tandem – Incorporates Trans-proteomic Pipeline (TPP) from ISB – NCI caBIG TM silver level compliant – Supports custom analytic tools (e.g., Q3 quantitation) – Runs on all common server operating systems & hardware – IT-friendly: LDAP, SASL, databases choice, simple config, etc. – Exports results to Excel, various text formats

8. How CPAS Addresses These Demands Integrate a wide variety of hardware & software Rapidly analyze many large MS/MS runs – Fred Hutchinson CPAS pipeline has processed: 67 thousand MS/MS fractions of 215 million spectra Individual runs of 300 fractions and 2 million spectra Millions of spectra per day on a regular basis

9. How CPAS Addresses These Demands Integrate a wide variety of hardware & software Rapidly analyze many large MS/MS runs Manage large volumes of results – All data organized by lab, folder, and experiment – Results are organized automatically by pipeline – Provides easy reorganization – Sophisticated cross-experiment query capabilities – Fred Hutchinson: 31 thousand runs, 260 million peptides

10. How CPAS Addresses These Demands Integrate a wide variety of hardware & software Rapidly analyze many large MS/MS runs Manage large volumes of results Collaborate easily while keeping data secure – CPAS system can be shared on intranet or Internet – Access requires just a browser and proper credentials – Keeps sensitive, unpublished scientific data secure – Provides various publishing and export options

11. What Is CPAS? Free, open source software connected to your… – Instruments – Search engine cluster – Analytic pipeline – Network file system …that provides a single, easy-to-use interface for: – Submitting and monitoring pipeline jobs – Managing your data – Answering biologically interesting questions about results

12. CPAS Pipeline Automated pipeline moves MS2 data from instrument, through MS/MS search and post-processing, and into CPAS MS/MS Search Cluster PC #40 X! Tandem, SEQUEST, MASCOT XPRESS, Peptide/Protein Prophet Sample Input Raw File mzXML, pepXML, protXML Files CPAS Convert Server mzXML File LCQ MALDI Sample Input Raw File LTQ FT Sample Input Raw File

13. Basic Analysis Features Load results produced by Mascot, SEQUEST, X! Tandem Inspect individual MS/MS spectra Filter and sort results based on peptide and protein characteristics: – Search engine scores, PeptideProphet, delta mass, modifications – Sequence mass, sequence coverage, gene, ProteinProphet Analyze peptide & protein quantitation Group results by protein or ProteinProphet groups Customize columns, save favorite filters and views Export filtered results to Excel, TSV, DTA, PKL, AMT formats

14. Advanced Analysis Features Filter groups of runs and compare peptides, proteins, ProteinProphet, quantitation, etc Analyze groups of runs based on sample properties Search all experiments for a specific protein or gene name Link results to protein annotations – Load protein knowledgebases: TrEMBL, Swiss-Prot – Gene Ontology: produce GO charts analyzing molecular function, cellular location, metabolic process – Custom protein annotation lists Flexible, custom query capability – Join results to differ – Display exactly the data you care about

15. Experimental Annotations Standards-based annotation of experiments Data/experiment exchange format See tutorial on http://www.labkey.org

16. Demo

17. What Does “Apache 2.0 Open Source” Mean? The product is free All source code is available for your review You can modify and extend the product You can contribute changes back (or not) You can re-distribute source or product (modified or not) Broad development community is emerging

18. LabKey Software, Inc. Private consulting company created by FHCRC and team of software professionals – Formed to support, document, and extend the CPAS project to other functions and labs – Independent company to directly address other institutions’ needs and secure outside funding Partnership: – Clients provide scientific leadership – LabKey focuses on software development LabKey is available to customize, install, and support your pipeline, CPAS, and other LabKey applications – Business model ensures you get help & support when you need it

19. Resources http://www.labkey.org – CPAS Distribution & Support Site – Ask questions, contribute feedback – Peruse all the CPAS documentation & tutorials – Download the latest version (LabKey 2.1) Graphical installer for Windows installation Well documented “manual” installation for Linux/Mac http://www.labkey.com – LabKey Software Inc. company web site CPAS Paper – Rauch A, Bellew M, Eng J, et al. Computational Proteomics Analysis System (CPAS): An Extensible, Open-source Analytic System for Evaluating and Publishing Proteomic Data and High throughput Biological Experiments. J Proteome Res 2006;5(1):112-121.

20. Next Steps Visit our booth Join our informal receptions here – 6:30 – 9:30PM Mon, Tue, Wed Install CPAS and give it a test drive – http://www.labkey.org – USB key

21. Acknowledgements Fred Hutchinson Cancer Research Center National Cancer Institute Canary Foundation Gates Foundation Institute for Systems Biology Ron Beavis & The GPM Numerous developer contributors

22. Questions?