Computational Mass Spectrometry @ Pacific Northwest National Laboratory's repositories
Thermo-Raw-File-Reader
.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific
DeconTools
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
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.
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.
Formultitude
Software for the assignment of low weight molecular formulas from high-resolution mass spectra.
Thermo-FAIMS-to-MzML
Converts a Thermo .raw file with FAIMS scans into a series of .mzML files, creating one .mzML file for each FAIMS compensation voltage (CV) value.
PSI-Interface
C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.
DBSchema_MTS
PRISM Mass and Time Tag System database schema
MyEMSL-Reader
MyEMSL Reader
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.github.io
Markdown files displayed at https://pnnl-comp-mass-spec.github.io/
PNNL-PreProcessor
Distribution binaries for the PNNL PreProcessor
PNNL.DMS.utils
Tools to interface with PNNL's DMS in R
SAIS-CSharp
Suffix array, induced sorting library. Source from https://sites.google.com/site/yuta256/sais, with updated project and framework configuration
UIMF-Library
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)
DMS-Organism-Database-Handler
Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application
MaxQuant-Param-File-Mod-Extractor
Parses a MaxQuant parameter file (XML-based) to extract the nodes that define static and dynamic mods.
mediawiki-extensions-CirrusSearch
🔍 Mirror of https://gerrit.wikimedia.org/g/mediawiki/extensions/CirrusSearch. See https://www.mediawiki.org/wiki/Developer_access for contributing.
NTRK-Experiment-19
Scripts for experiment 19 analysis
PNNL.DIA.utils
**WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects
Protein-File-Reader
Class for reading Protein files, specifically .fasta files and certain tab-delimited formats
RDF-Taxonomy-Converter
Processes an RDF taxonomy file and creates a tab-delimited text file with the extracted taxonomy terms
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.