U.S. Department of Energy

Pacific Northwest National Laboratory

MS/MS Analysis Tools

GlyQ-IQ

GlyQ-IQ is software that performs a targeted, chromatographic centric search of mass spectral data for glycans. The software uses a list of glycan targets to search for expected features in MS1 spectra.

Area of Research: 
Proteomics,

PE-MMR

PE-MMR can be used to create a MGF file with refined parent ion masses and charges, which can lead to more accurate search results from MS/MS spectra.

Area of Research: 
Proteomics,

MZRefinery

MZRefinery is a software tool for correcting systematic mass error biases in mass spectrometry data files.

Area of Research: 
Proteomics,

MSGFPlus/MASIC Data Processing Toolbox

DataProcessing toolbox for running MSGF+ and MASIC, then merging the results. Uses Windows batch files to automate the process for a folder of Thermo .Raw files

Area of Research: 
Proteomics,

MSPathFinder

MSPathFinder is a database search engine for top-down proteomics, part of the Informed Proteomics package.

Area of Research: 
Proteomics
Informatics

MS-GF+

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Area of Research: 
Proteomics,

DeconMSn

DeconMSn creates spectrum files for tandem mass spectrometry data.

Area of Research: 
Proteomics,

Peptide Hit Results Processor

Converts a MSGF+ TSV file, X!Tandem results file (XML format), or a SEQUEST Synopsis/First Hits file to a series of tab-delimited text files summarizing the results.

Area of Research: 
Proteomics,

MASIC Results Merger

Reads the contents of a tab-delimited peptide hit results file (e.g.

Area of Research: 
Proteomics,

MASIC

MASIC (MS/MS Automated Selected Ion Chromatogram generator) Generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis.

Area of Research: 
Proteomics,
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