Repositories list

• DBSchema_PgSQL_DMS

  Public
  PRISM Data Management System PostgreSQL database schema

  PLpgSQL

  •0•3•0•0•Updated May 29, 2025May 29, 2025

• DMS-Website

  Public
  DMS Website

  PHP

  •0•1•0•1•Updated May 28, 2025May 28, 2025

• UIMF-Library

  Public
  Used to create, modify and extract data from UIMF files, which are SQLite databases of mass spectrometry data acquired at Pacific Northwest National Laboratory (PNNL)

  C#

  •

  Other

  •4•1•0•0•Updated May 28, 2025May 28, 2025

• SAIS-CSharp

  Public
  Suffix array, induced sorting library. Source from https://sites.google.com/site/yuta256/sais, with updated project and framework configuration

  C#

  •

  Other

  •1•1•0•0•Updated May 28, 2025May 28, 2025

• Protein-File-Reader

  Public
  Class for reading Protein files, specifically .fasta files and certain tab-delimited formats

  mass-spectrometryfasta-sequencesfasta

  C#

  •1•0•0•0•Updated May 28, 2025May 28, 2025

• PRISM-Class-Library

  Public
  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#

  •2•2•0•0•Updated May 28, 2025May 28, 2025

• DMS-Analysis-Manager

  Public
  DMS Analysis Tool Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated May 21, 2025May 21, 2025

• DMS-Capture-Task-Manager

  Public
  DMS Capture Task Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated May 17, 2025May 17, 2025

• ROSMAP103_TopDown

  Public
  R

  •0•0•0•0•Updated May 7, 2025May 7, 2025

• Buzzard

  Public
  Utility for manually and automatically adding datasets to DMS

  C#

  •0•0•0•0•Updated May 2, 2025May 2, 2025

• MSnSet.utils

  Public
  custom wrappers of frequently used R code

  R

  •8•7•2•0•Updated Apr 29, 2025Apr 29, 2025

• 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.

  C#

  •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

• Mage

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

  C#

  •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

• DMS-Instrument-Directory-Scanner

  Public
  Instrument directory scanner

  C#

  •0•0•0•1•Updated Apr 23, 2025Apr 23, 2025

• Package_Folder_Create_Manager

  Public
  Creates a new storage folder for newly created data packages

  C#

  •0•0•0•1•Updated Apr 23, 2025Apr 23, 2025

• Status-Message-DB-Updater

  Public
  Reads manager status messages from an ActiveMQ server and push them into the DMS database.

  C#

  •0•0•0•1•Updated Apr 23, 2025Apr 23, 2025

• AqMD3-Acquisition-Console

  Public
  Acquisition software for the Acqiris SA220P digitizer card

  C++

  •

  BSD 2-Clause "Simplified" License

  •1•3•0•1•Updated Apr 22, 2025Apr 22, 2025

• protein-coverage-summarizer

  Public
  Computes 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.

  protein-sequencesfastamass-spectrometry+ 1protein-sequence

  C#

  •

  BSD 2-Clause "Simplified" License

  •3•6•0•0•Updated Apr 22, 2025Apr 22, 2025

• MyEMSL-Reader

  Public
  MyEMSL Reader

  C#

  •0•2•0•0•Updated Apr 21, 2025Apr 21, 2025

• 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).

  mass-spectrometryms-spectrum

  C#

  •3•17•4•0•Updated Apr 16, 2025Apr 16, 2025

• DMS-Space-Manager

  Public
  DMS Space Manager

  C#

  •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

• DataPackage-Archive-Manager

  Public
  DataPackage Archive Manager

  C#

  •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

• VSProj-NuGet-Version-Updater

  Public
  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#

  •0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

• PSI-Interface

  Public
  C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.

  mass-spectrometrymzmlmzidentml+ 1mzml-files

  C#

  •3•4•0•0•Updated Apr 15, 2025Apr 15, 2025

• 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.

  mass-spectrometryms-spectrum

  C#

  •3•9•1•0•Updated Apr 12, 2025Apr 12, 2025

• PNNL.DIA.utils

  Public
  **WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects

  R

  •

  Other

  •1•0•3•0•Updated Apr 11, 2025Apr 11, 2025

• Mzid-To-Tsv-Converter

  Public
  Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.

  mass-spectrometrymzidentmlmzid

  C#

  •2•6•3•0•Updated Apr 10, 2025Apr 10, 2025

• MzidMerger

  Public
  Merges split-FASTA MS-GF+ search result .mzid files.

  mass-spectrometrymzidentmlmzid

  C#

  •0•3•0•0•Updated Apr 10, 2025Apr 10, 2025

• PPMErrorCharter

  Public
  Utility for generating plots of the mass measurement errors before and after processing with mzRefinery

  mass-spectrometry

  C#

  •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• 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.

  mass-spectrometry

  C#

  •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025