U.S. Department of Energy

Pacific Northwest National Laboratory

Proteomics,

Thermo Raw File Reader

The Thermo Raw File Reader is a .NET DLL that demonstrates how to read Thermo-Finnigan .Raw files using Thermo's MS File Reader.

Area of Research: 
Proteomics,

Protein Sequence Motif Extractor

The Protein Sequence Motif Extractor reads a fasta file or tab delimited file containing protein sequences, then looks for the specified motif in each protein sequence.

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,

MS File Info Scanner

The MS File Info Scanner can be used to scan a series of MS data files (or data folders) and extract the acquisition start and end times, number of spectra, and the total size of the data.

Area of Research: 
Proteomics,

VIPER

VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses.

Area of Research: 
Proteomics,

Protein Coverage Summarizer

The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified.

Area of Research: 
Proteomics,

MTDB Creator

This software can be used to generate an Accurate Mass and Time tag database from local MS/MS search engine results from MSGF+, X!Tandem, or SEQUEST.  It can create the database in two formats:

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,

DtaRefinery

Reduces mass measurement errors for parent ions of tandem MS/MS data by modeling systematic errors based on putative peptide identifications. This information is used to subtract out errors from parent ion protonated m

Area of Research: 
Proteomics,

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