ProteoSAFe: Proteomics Scalable, Accessible and Flexible Environment

The CCMS ProteoSAFe platform is designed for simplified integration of new tools (Flexibility) which can be easily accessed (Accessibility) and executed on laptops or large compute clusters (Scalability).

ProteoSAFe

Software Tools & Datasets

ProteoSAFe: Main site
ProteoSAFe Early Access: Beta test site
MassIVE: Data repository site

Key Publications

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Moree WJ, Phelan VV, Wu CH, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13811-6. doi: 10.1073/pnas.1206855109.
The generating function approach for peptide identification in spectral networks Guthals A., Christina B. Bandeira N. Research in Computational Molecular Biology, Lecture Notes in Computer Science; (8394) 85-99
An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays. Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. Mol Cell Proteomics. 2014 Jan;13(1):157-67. doi: 10.1074/mcp.M113.031260. Epub 2013 Oct 18.
UniNovo: a universal tool for de novo peptide sequencing. Jeong K, Kim S, Pevzner PA. Bioinformatics. 2013 Aug 15;29(16):1953-62. doi: 10.1093/bioinformatics/btt338. Epub 2013 Jun 12.
Peptide identification from mixture tandem mass spectra. Wang J, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N. Mol Cell Proteomics. 2010 Jul;9(7):1476-85. doi: 10.1074/mcp.M000136-MCP201. Epub 2010 Mar 27.
Protein identification by spectral networks analysis. Bandeira N. Methods Mol Biol. 2011;694:151-68. doi: 10.1007/978-1-60761-977-2_11.
View All CCMS Publictions

While many mass-spectrometry (MS) software tools are freely available, the large majority of them are designed to solve small, well-defined problems and require complex manual steps to translate data into meaningful biological results. Users have to learn how to install and use each tool and need to be aware of all the possible pitfalls of connecting disparate algorithms that were not designed to work together, often resulting in exceedingly high False Discovery Rates or missing many positive identifications. ProteoSAFe is a software platform designed to bridge this gap by allowing bioinformaticians to integrate their novel algorithms into workflows (Flexibility), which are then seamlessly executable on either desktops or compute clusters (Scalability), and easily accessed via a user-friendly interface (Accessibility).

Since its inception, ProteoSAFe has already enabled searching over 1.3 billion spectra in over 28,000 searches from over 4,000 users. To the best of our knowledge, ProteoSAFe integrates the most diverse set of algorithms and tools under a single platform and makes these freely available for online searches run on the CCMS compute cluster (see Software Tools and Datasets on this page) . More details on available workflows are available on the CCMS Software Tools page.