@PNNL-Comp-Mass-Spec

Computational Mass Spectrometry @ Pacific Northwest National Laboratory

  • PRISM Data Management System database schema

    SQLPL 1 2 Updated Oct 20, 2018
  • The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

    Visual Basic 1 BSD-2-Clause Updated Oct 19, 2018
  • DMS Analysis Tool Manager

    C# BSD-2-Clause Updated Oct 19, 2018
  • DMS Capture Task Manager

    C# BSD-2-Clause Updated Oct 19, 2018
  • The FASTA File Splitter program can be used to split apart a protein FASTA file into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.

    Visual Basic 1 Updated Oct 19, 2018
  • The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.

    C# Updated Oct 18, 2018
  • DataPackage Archive Manager

    C# Updated Oct 17, 2018
  • Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.

    C# 1 Updated Oct 17, 2018
  • Utility for generating plots of the mass measurement errors before and after processing with mzRefinery

    C# Updated Oct 17, 2018
  • Tool to merge split-fasta MS-GF+ search result mzids.

    C# Updated Oct 17, 2018
  • C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.

    C# 1 1 Updated Oct 17, 2018
  • This program pings computers on Bionet to see which respond. It then optionally contacts DMS with the list of active hosts.

    C# Updated Oct 16, 2018
  • This program inspects a .NET DLL or .Exe to determine the version. This allows a 32-bit .NET application to call this program via the command prompt to determine the version of a 64-bit DLL or Exe.

    Visual Basic Updated Oct 16, 2018
  • Instrument directory scanner

    C# Updated Oct 16, 2018
  • DMS EMail Manager

    C# Updated Oct 16, 2018
  • MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis. The SICs are generated using the LC-MS data, then each SIC is processed using a peak finding algorithm to characterize the chromatographic peaks, providing peak statistics including elution time of the peak apex, peak ar…

    Visual Basic 2 Updated Oct 16, 2018
  • The Cyclops library can be used to apply a workflow of data analysis steps to data stored in a SQLite database

    C# Updated Oct 16, 2018
  • The Mage suite of tools provide access to DMS files and metadata.

    C# Updated Oct 16, 2018
  • Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).

    C# Updated Oct 16, 2018
  • The AScore program can process first-hits or synopsis files from MSGF+, SEQUEST, or X!Tandem to compute confidence scores for the position of phosphorylated residues.

    C# Updated Oct 16, 2018
  • Parses a FASTA file (with protein name and sequence information) to check for valid text. Also returns protein and residue stats.

    Visual Basic 1 Updated Oct 16, 2018
  • Class for reading Protein files, specifically .fasta files and certain tab-delimited formats

    C# 1 Updated Oct 16, 2018
  • Searches for Visual Studio project files (.csproj and.vsproj) that reference a specific NuGet package and updates the referenced version to a newer version if necessary.

    C# Updated Oct 15, 2018
  • .NET DLL wrapper for Thermo's MS File Reader, which is accessible by creating an account at https://thermo.flexnetoperations.com/control/thmo/login then logging in and choosing "Utility Software"

    C# 4 3 Updated Oct 11, 2018
  • Program that implements a protein parsimony algorithm for grouping proteins with similar peptides.

    C# Updated Oct 11, 2018
  • The Peptide Hit Results Processor can be used to convert an X!Tandem results file (XML format), MSGF+ .tsv results file, or SEQUEST synopsis file (or first hits file) to a series of tab-delimited text files summarizing the results.

    C# Updated Oct 11, 2018
  • DMS Update Manager

    C# Updated Oct 11, 2018
  • 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. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.

    C# 1 Updated Oct 11, 2018
  • MyEMSL Reader

    C# 1 Updated Oct 11, 2018
  • LCMSNet software for instrument control

    C# 1 1 Updated Oct 8, 2018
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