Pinned Repositories
AutoCCS
Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry
DB-Schema-Export-Tool
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 and logins. The program can also export table data to create SQL files with an Insert Into statement for each row.
DeconTools
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
Informed-Proteomics
Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
LIQUID
Software tool for identifying lipids in LC-MS/MS-based lipidomics data
MASIC
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).
Molecular-Weight-Calculator-DLL
The Molecular Weight Calculator can be used to calculate the molecular weight and percent composition of chemical formulas and amino acids (peptides). It includes several other utility modules and is available as both a GUI version and a C# DLL version.
Molecular-Weight-Calculator-VB6
Molecular Weight Calculator (MWTWin): Graphical program written in VB6 with numerous mass calculation utilities.
MS-File-Info-Scanner
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.
Thermo-Raw-File-Reader
.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific
Computational Mass Spectrometry @ Pacific Northwest National Laboratory's Repositories
PNNL-Comp-Mass-Spec/DeconTools
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
PNNL-Comp-Mass-Spec/MASIC
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/AutoCCS
Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry
PNNL-Comp-Mass-Spec/MS-File-Info-Scanner
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.
PNNL-Comp-Mass-Spec/DeconEngineV2
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
PNNL-Comp-Mass-Spec/MSnSet.utils
custom wrappers of frequently used R code
PNNL-Comp-Mass-Spec/TopPICR
R package for processing results from TopPIC, including resolving ambiguity in proteoform identification
PNNL-Comp-Mass-Spec/DBSchema_DMS
PRISM Data Management System database schema
PNNL-Comp-Mass-Spec/DBSchema_PgSQL_DMS
PRISM Data Management System PostgreSQL database schema
PNNL-Comp-Mass-Spec/DMS-Analysis-Manager
DMS Analysis Tool Manager
PNNL-Comp-Mass-Spec/LCMSNet
LCMSNet software for instrument control
PNNL-Comp-Mass-Spec/AmpsSDK
SDK for controlling the Adaptable Multiple Power Supplies (AMPS boxes)
PNNL-Comp-Mass-Spec/BrukerDataReader
Bruker data reader
PNNL-Comp-Mass-Spec/PlexedPiper
PNNL-Comp-Mass-Spec/PNNL-PreProcessor
Distribution binaries for the PNNL PreProcessor
PNNL-Comp-Mass-Spec/PRISM-Class-Library
The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.
PNNL-Comp-Mass-Spec/DMS-Capture-Task-Manager
DMS Capture Task Manager
PNNL-Comp-Mass-Spec/DMS-Website
DMS Website
PNNL-Comp-Mass-Spec/PHRP
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/PNNL.DMS.utils
Tools to interface with PNNL's DMS in R
PNNL-Comp-Mass-Spec/Sipper
Used to automatically detect and quantify partially labeled C13 peptides in a mass spectrometry dataset.
PNNL-Comp-Mass-Spec/DMS-Dataset-Retriever
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-Organism-Database-Handler
Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application
PNNL-Comp-Mass-Spec/DMS-Space-Manager
DMS Space Manager
PNNL-Comp-Mass-Spec/Mage
The Mage suite of tools provide access to DMS files and metadata.
PNNL-Comp-Mass-Spec/Parameter-File-Editor
DLL for retrieving parameter files from DMS
PNNL-Comp-Mass-Spec/PNNL.DIA.utils
**WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects
PNNL-Comp-Mass-Spec/proteomics_therapy
Collection of lessons from IO group's data analysis workshops (i.e. TheRa.py Sessions)
PNNL-Comp-Mass-Spec/ROSMAP103_TopDown
PNNL-Comp-Mass-Spec/VSProj-NuGet-Version-Updater
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.