Projects

BatMass: mass-spec data visualization

A framework for LC-MS data visualization and exploration. View spectra, extracted ion chromatograms and 2D ion maps of LC-MS experiments. Synchronized viewers.

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.

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.

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.

IMTBX+Grppr: Ion Mobility Toolbox + Isotopic Grouping

A suite of tools for extracting signals from Ion Mobility (IM) data (IM-MS, LC-IM-MS) and performing isotopic envelopes detection.

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.