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@PNNL-Comp-Mass-Spec

Computational Mass Spectrometry @ Pacific Northwest National Laboratory

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  1. Thermo-Raw-File-Reader Thermo-Raw-File-Reader Public

    .NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific

    C# 42 15

  2. Informed-Proteomics Informed-Proteomics Public

    Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data

    C# 32 9

  3. LIQUID LIQUID Public

    Software tool for identifying lipids in LC-MS/MS-based lipidomics data

    C# 23 2

  4. DeconTools DeconTools Public

    Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.

    C# 20 5

  5. MASIC MASIC Public

    MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis, characterizing the peak(s) in each SIC, computing peak statistics incl…

    C# 19 2

  6. DB-Schema-Export-Tool DB-Schema-Export-Tool Public

    Exports SQL Server and Postgres database objects as schema files. Exported objects include tables, views, stored procedures, and functions, plus also database properties including database roles an…

    C# 16 9

Repositories

Showing 10 of 184 repositories
  • IMS-Informed-Library Public

    ImsInformed is a .NET class library that provides target identification workflows for peptides and metabolites alike in IMS experiment runs.

    PNNL-Comp-Mass-Spec/IMS-Informed-Library's past year of commit activity
    C# 2 0 1 0 Updated Oct 1, 2026
  • MS-Data-File-Reader Public

    A VB.NET DLL that can read mass spectrometry data from four file formats: mzXML, mzData, concatenated .dta files (_dta.txt), and Mascot Generic Format files (.mgf)

    PNNL-Comp-Mass-Spec/MS-Data-File-Reader's past year of commit activity
    C# 3 3 1 0 Updated Oct 1, 2026
  • PNNL-Omics Public

    Data analysis, file I/O, and visualization routines used by several of the omics-related software developed at PNNL

    PNNL-Comp-Mass-Spec/PNNL-Omics's past year of commit activity
    C# 0 1 1 0 Updated Oct 1, 2026
  • Uniprot-DAT-File-Parser Public

    This program can read a Uniprot .Dat file and parse out the information for each entry, creating a tab delimited text file or a FASTA file.

    PNNL-Comp-Mass-Spec/Uniprot-DAT-File-Parser's past year of commit activity
    Visual Basic .NET 6 1 0 0 Updated Oct 1, 2026
  • DMS-Website Public

    DMS Website

    PNNL-Comp-Mass-Spec/DMS-Website's past year of commit activity
    JavaScript 1 0 0 2 Updated Sep 30, 2026
  • DMS-Analysis-Manager Public

    DMS Analysis Tool Manager

    PNNL-Comp-Mass-Spec/DMS-Analysis-Manager's past year of commit activity
    C# 3 BSD-2-Clause 0 0 0 Updated Sep 29, 2026
  • Peptide-Fragmentation-Modeller Public

    The Peptide Fragmentation Modeller is a command-line utility reads that reads in a text file of peptide sequences and generates the theoretical fragmentation pattern for each, outputting the results in a single concatenated DTA file, or in separate .Dta files. The ion intensity values are not predicted values; instead, b, c, y, and z ions are as…

    PNNL-Comp-Mass-Spec/Peptide-Fragmentation-Modeller's past year of commit activity
    Visual Basic .NET 1 2 1 0 Updated Sep 29, 2026
  • LC-MS-Feature-Finder Public

    Finds LC-MS features using deisotoped data from DeconTools

    PNNL-Comp-Mass-Spec/LC-MS-Feature-Finder's past year of commit activity
    Visual Basic .NET 0 0 1 0 Updated Sep 29, 2026
  • PepAligner Public

    The PepAligner program can read a file containing peptides and align them to a file of protein sequences (.Fasta or delimited text) using Smith-Waterman alignment.

    PNNL-Comp-Mass-Spec/PepAligner's past year of commit activity
    Visual Basic .NET 1 2 1 0 Updated Sep 28, 2026
  • MS-File-Info-Scanner Public

    Examines a series of MS data files (or data directories) and extracts the acquisition start and end times, number of spectra, and the total size of the data. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.

    PNNL-Comp-Mass-Spec/MS-File-Info-Scanner's past year of commit activity
    C# 9 3 1 0 Updated Sep 23, 2026
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