proteomics

MSFragger: Ultra-fast proteomics search engine
Ultra-fast proteomics search engine. Regular searches - when the precursor mass is limited to a narrow window of several ppm - are done within a few seconds. An “open-search” (with large precursor mass range tolerance, e.g. +/-500 Da) for a 2 hour LC gradient bottom-up proteomics experiment can be done in a minute or so on a laptop.
Website GitHub Manuscript
MSFragger: Ultra-fast proteomics search engine
MSFTBX: MS File Toolbox
A fast Java library for mass spectrometry data files access (mzML, mzXML, pepXML, protXML, mzId, mzIdentML, etc). Writers for some formats are also available. Available on Maven Central.
Maven Central GitHub Manuscript
MSFTBX: MS File Toolbox
FragPipe: Proteomics 0-60 in 5 seconds
A cross-platform pipeline for comprehensive analysis of LC/MS proteomics data. Graphical User Interface (GUI) for running MSFragger (search engine), Philosopher (peptide and protein validation, reports), qunatitation tools, spectral library building and more.
Website GitHub
FragPipe: Proteomics 0-60 in 5 seconds
DeltaMass: view and interrogate open search proteomics data
View and interrogate open search proteomics data.
Code Manuscript
DeltaMass: view and interrogate open search proteomics data
DIA-Umpire
Data Independent Acquisition (DIA) data processing tool that doens’t require a spectral library. Detects features in MS1 and MS2, correlates precursors to fragments based on elution profile and compiles pseudo-MS/MS spectra which can be searched with standard proteomic search tools.
Website Code Manuscript
DIA-Umpire