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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# 38 12

  2. Informed-Proteomics Informed-Proteomics Public

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

    C# 29 9

  3. LIQUID LIQUID Public

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

    C# 19 2

  4. DeconTools DeconTools Public

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

    C# 18 4

  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# 15 4

  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# 12 8

Repositories

Showing 10 of 183 repositories
  • DMS-Dataset-Retriever Public

    Copies DMS instrument data files to a local computer, organizing the files into subdirectories, and optionally renaming the files to use a new dataset name.

    PNNL-Comp-Mass-Spec/DMS-Dataset-Retriever’s past year of commit activity
    C# 0 0 0 0 Updated Nov 9, 2024
  • PlexedPiper Public Forked from vladpetyuk/PlexedPiper
    PNNL-Comp-Mass-Spec/PlexedPiper’s past year of commit activity
    R 2 7 1 2 Updated Nov 9, 2024
  • DMS-Website Public

    DMS Website

    PNNL-Comp-Mass-Spec/DMS-Website’s past year of commit activity
    PHP 1 0 0 1 Updated Nov 8, 2024
  • 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 Nov 8, 2024
  • LCMSNet Public

    LCMSNet software for instrument control

    PNNL-Comp-Mass-Spec/LCMSNet’s past year of commit activity
    C# 3 1 0 0 Updated Nov 7, 2024
  • PHRP Public

    Converts a MS-GF+ .tsv search result file or an X!Tandem results file (XML format) into a series of tab-delimited text files, summarizing the results. It also supports results files from MaxQuant, MSAlign, TopPIC, MODa, MODPlus, and MSPathFinder, along with SEQUEST Synopsis/First Hits files.

    PNNL-Comp-Mass-Spec/PHRP’s past year of commit activity
    C# 0 0 0 0 Updated Nov 7, 2024
  • DBSchema_PgSQL_DMS Public

    PRISM Data Management System PostgreSQL database schema

    PNNL-Comp-Mass-Spec/DBSchema_PgSQL_DMS’s past year of commit activity
    PLpgSQL 3 0 0 0 Updated Nov 6, 2024
  • Mage Public

    The Mage suite of tools provide access to DMS files and metadata.

    PNNL-Comp-Mass-Spec/Mage’s past year of commit activity
    C# 0 0 0 0 Updated Nov 6, 2024
  • 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 including elution time of the peak apex, peak area, and peak signal/noise. It can also extract reporter ion abundances (e.g. iTRAQ or TMT).

    PNNL-Comp-Mass-Spec/MASIC’s past year of commit activity
    C# 15 4 4 0 Updated Nov 6, 2024
  • TopPICR Public

    R package for processing results from TopPIC, including resolving ambiguity in proteoform identification

    PNNL-Comp-Mass-Spec/TopPICR’s past year of commit activity
    R 4 GPL-3.0 2 0 0 Updated Nov 2, 2024
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