Fast and Sensitive Proteome Analysis
In a 2014 publication, we described a method for the near complete analysis of the yeast proteome in just one hour. However, achieving a comparable coverage of mammalian proteomes requires spending hours or even days of analysis time. Improved peptide separation technologies, along with advancements in MS hardware, will be essential for achieving this goal. We and others are actively working towards improving the speed, depth, and sensitivity at which proteomes can be measured.
Interactive Peptide Spectral Annotator (IPSA)
A web-based utility for the annotation of shotgun proteomics mass spectrometry data. IPSA generates interactive visualizations from bottom-up proteomic workflows. These visualizations can be exported in SVG format and annotated fragment ions and additional metrics can be exported in CSV format.
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MS-Helios
An easy to use command line tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps. MS-Helios automatically generates data and configuration files to create high quality and publishable circular plots with Circos.
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Compass
A free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. COMPASS supports all functions required for searching proteomics data including: FASTA database creation, peptide-spectral matching, calculation of false discovery rates, and protein grouping.
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