Repositories list

• MSnSet.utils

  Public
  custom wrappers of frequently used R code

  R

  •8•5•4•0•Updated Jan 15, 2025Jan 15, 2025

• PNNL.DMS.utils

  Public
  Tools to interface with PNNL's DMS in R

  dmspnnl

  R

  •0•1•4•1•Updated Jan 15, 2025Jan 15, 2025

• 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 Jan 15, 2025Jan 15, 2025

• PNNL.DIA.utils

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

  R

  •

  Other

  •1•0•2•0•Updated Jan 14, 2025Jan 14, 2025

• DBSchema_DMS

  Public
  PRISM Data Management System database schema

  TSQL

  •3•3•0•0•Updated Jan 12, 2025Jan 12, 2025

• DBSchema_PgSQL_DMS

  Public
  PRISM Data Management System PostgreSQL database schema

  PLpgSQL

  •0•3•0•0•Updated Jan 12, 2025Jan 12, 2025

• DLL-Version-Inspector

  Public
  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.

  C#

  •0•0•0•0•Updated Jan 11, 2025Jan 11, 2025

• DMS-Analysis-Manager

  Public
  DMS Analysis Tool Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated Jan 11, 2025Jan 11, 2025

• DMS-Capture-Task-Manager

  Public
  DMS Capture Task Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Jan 11, 2025Jan 11, 2025

• DMS-Website

  Public
  DMS Website

  PHP

  •0•1•0•1•Updated Jan 9, 2025Jan 9, 2025

• MyEMSL-Reader

  Public
  MyEMSL Reader

  C#

  •0•2•0•0•Updated Dec 26, 2024Dec 26, 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 Dec 22, 2024Dec 22, 2024

• Protein-Parsimony

  Public
  Program that implements a protein parsimony algorithm for grouping proteins with similar peptides.

  mass-spectrometry

  C#

  •0•0•1•0•Updated Dec 21, 2024Dec 21, 2024

• Mage

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

  C#

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• AutoCCS

  Public
  Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry

  mass-spectrometry

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•8•1•0•Updated Dec 13, 2024Dec 13, 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 Dec 7, 2024Dec 7, 2024

• AmpsSDK

  Public
  SDK for controlling the Adaptable Multiple Power Supplies (AMPS boxes)

  C#

  •

  MIT License

  •3•2•0•0•Updated Dec 6, 2024Dec 6, 2024

• LCMSNet

  Public
  LCMSNet software for instrument control

  C#

  •1•3•0•0•Updated Nov 27, 2024Nov 27, 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

• 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

• 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

• 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#

  •5•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

• 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