Repositories list

• PNNL.DMS.utils

  Public
  Tools to interface with PNNL's DMS in R

  dmspnnl

  R

  •0•1•5•0•Updated Nov 24, 2024Nov 24, 2024

• DMS-Analysis-Manager

  Public
  DMS Analysis Tool Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated Nov 24, 2024Nov 24, 2024

• DBSchema_PgSQL_DMS

  Public
  PRISM Data Management System PostgreSQL database schema

  PLpgSQL

  •0•3•0•0•Updated Nov 24, 2024Nov 24, 2024

• LCMSNet

  Public
  LCMSNet software for instrument control

  C#

  •1•3•0•0•Updated Nov 23, 2024Nov 23, 2024

• DMS-Website

  Public
  DMS Website

  PHP

  •0•1•0•1•Updated Nov 22, 2024Nov 22, 2024

• 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 Nov 21, 2024Nov 21, 2024

• PlexedPiper

  Public
  proteomicsisobaric-labeling

  R

  •7•2•1•2•Updated Nov 20, 2024Nov 20, 2024

• DBSchema_DMS

  Public
  PRISM Data Management System database schema

  TSQL

  •3•3•0•0•Updated Nov 16, 2024Nov 16, 2024

• Mage

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

  C#

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• PNNL-PreProcessor

  Public
  Distribution binaries for the PNNL PreProcessor

  0•2•0•0•Updated Nov 14, 2024Nov 14, 2024

• ROSMAP103_TopDown

  Public
  R

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• 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 Nov 9, 2024Nov 9, 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.

  mass-spectrometry

  C#

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 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).

  mass-spectrometryms-spectrum

  C#

  •4•15•4•0•Updated Nov 6, 2024Nov 6, 2024

• TopPICR

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

  R

  •

  GNU General Public License v3.0

  •2•4•0•0•Updated Nov 2, 2024Nov 2, 2024

• Sipper

  Public
  Used to automatically detect and quantify partially labeled C13 peptides in a mass spectrometry dataset.

  mass-spectrometryms-spectrum

  C#

  •1•1•0•0•Updated Nov 1, 2024Nov 1, 2024

• BrukerDataReader

  Public
  Bruker data reader

  C#

  •0•2•0•0•Updated Nov 1, 2024Nov 1, 2024

• DeconTools

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

  mass-spectrometryms-spectrum

  C#

  •4•18•2•0•Updated Oct 31, 2024Oct 31, 2024

• DeconEngineV2

  Public
  The DeconEngine includes routines for deconvoluting (deisotoping) observed isotopic signatures in mass spectrometry data to detect features. The releases include Zip files with DeconMSn.exe

  C++

  •1•5•0•0•Updated Oct 31, 2024Oct 31, 2024

• proteomics_therapy

  Public
  Collection of lessons from IO group's data analysis workshops (i.e. TheRa.py Sessions)

  TeX

  •1•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• PNNL.DIA.utils

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

  R

  •

  Other

  •1•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• DMS-Capture-Task-Manager

  Public
  DMS Capture Task Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Oct 18, 2024Oct 18, 2024

• DMS-Organism-Database-Handler

  Public
  Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application

  C#

  •1•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• Parameter-File-Editor

  Public
  DLL for retrieving parameter files from DMS

  Visual Basic .NET

  •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• 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•8•1•0•Updated Oct 1, 2024Oct 1, 2024

• 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 Sep 26, 2024Sep 26, 2024

• DMS-Space-Manager

  Public
  DMS Space Manager

  C#

  •0•0•0•0•Updated Sep 22, 2024Sep 22, 2024

• DataPackage-Archive-Manager

  Public
  DataPackage Archive Manager

  C#

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• MyEMSL-Reader

  Public
  MyEMSL Reader

  C#

  •0•2•0•0•Updated Sep 20, 2024Sep 20, 2024

• AScore

  Public
  The AScore program can process first-hits or synopsis files from MS-GF+, SEQUEST, or X!Tandem to compute confidence scores for the position of phosphorylated residues.

  mass-spectrometry

  C#

  •1•3•0•0•Updated Sep 18, 2024Sep 18, 2024