BatMass

A framework for LC-MS data visualization and exploration. View spectra, extracted ion chromatograms and 2D ion maps of LC-MS experiments. Synchronized viewers. Visualize DIA experiments. Overlay MS/MS events, peptide identifications or custom data (via delimited text files) over a 2D map. 🚀
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Selected Publications

Top-down proteomics has emerged as a transformative method for the analysis of protein sequence and post-translational modifications (PTMs). Top-down experiments have historically been performed primarily on ultra-high resolution mass spectrometers due to the complexity of spectra resulting from fragmentation of intact proteins, but recent advances in coupling ion mobility separations to faster, lower resolution mass analyzers now offer a viable alternative. However, software capable of interpreting the highly complex 2-dimensional spectra that result from coupling ion mobility separation to top-down experiments is currently lacking. In this manuscript we present a software suite consisting of 2 programs, IMTBX (IM Toolbox) and Grppr (Grouper), which enable fully automated processing of such data. We demonstrate the capabilities of this software suite by examining a series of intact proteins on a Waters Synapt G2 ion-mobility equipped mass spectrometer, and compare the results to the manual and semi-automated data analysis procedures we have used previously.
In Analytical Chemistry, 2017

We present a fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables a more than 100-fold improvement in speed over most existing proteome database search tools. Using several large proteomic data sets, we demonstrate how MSFragger empowers the open database search concept for comprehensive identification of peptides and all their modified forms, uncovering dramatic differences in modification rates across experimental samples and conditions.
In Nature Methods, 2017

The human brain interprets visual data much better than plain text, hence the saying “a picture is worth a thousand words”. Here, we present the BatMass software package, which allows for performing quick quality control of raw LC–MS data through its fast visualization capabilities. It also serves as a testbed for developers of LC–MS data processing algorithms by providing a data access library for open mass spectrometry file formats and a means of visually mapping processing results back to the original data. We illustrate the utility of BatMass with several use cases of quality control and data exploration.
In Journal of Proteome Research, 2016

DIA-Umpire (http://diaumpire.sourceforge.net/), a comprehensive computational workflow and open-source software for DIA data, detects precursor and fragment chromatographic features and assembles them into pseudo–tandem MS spectra. These spectra can be identified with conventional database-searching and protein-inference tools, allowing sensitive, untargeted analysis of DIA data without the need for a spectral library. Quantification is done with both precursor- and fragment-ion intensities. We demonstrated the performance of the method with control samples of varying complexity and publicly available glycoproteomics and affinity purification–MS data.
In Nature Methods, 2015

Projects

BatMass

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

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.

IMTBX+Grppr

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

MSFragger

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.

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.