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/Informed-Proteomics
Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
PNNL-Comp-Mass-Spec/LIQUID
Software tool for identifying lipids in LC-MS/MS-based lipidomics data
PNNL-Comp-Mass-Spec/AutoCCS
Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry
PNNL-Comp-Mass-Spec/LCMS-Spectator
LCMS raw data and MS-GF+ results viewer
PNNL-Comp-Mass-Spec/proteomics-data-analysis-tutorial
A comprehensive tutorial for proteomics data analysis in R that utilizes packages developed by researchers at PNNL and from Bioconductor.
PNNL-Comp-Mass-Spec/FAIMS-MzXML-Generator
Converts a Thermo .raw file with FAIMS scans into a series of .mzXML files, creating one .mzXML file for each FAIMS compensation voltage (CV) value.
PNNL-Comp-Mass-Spec/InfernoRDN
InfernoRDN can perform various downstream analyses on large scale datasets from proteomics and microarrays
PNNL-Comp-Mass-Spec/Kaiko
deep learning-based de novo peptide sequencing tool
PNNL-Comp-Mass-Spec/DL-Batch-Correction
PNNL-Comp-Mass-Spec/Fasta-Organism-Filter
Reads a protein FASTA file and filters the proteins by organism name, protein name, or taxonomy ID to create a new, filtered file.
PNNL-Comp-Mass-Spec/MASIC-Results-Merger
Merges the contents of a tab-delimited text file with peptide search results (e.g. from X!Tandem or MS-GF+) with the corresponding MASIC results files, appending the relevant MASIC stats for each PSM. Also supports reporter ion abundances.
PNNL-Comp-Mass-Spec/MTDB-Creator
Used to generate an Accurate Mass and Time tag database from local MS/MS search engine results (from SEQUEST, X!Tandem, or MS-GF+)
PNNL-Comp-Mass-Spec/OBO-Data-Converter
Utility for converting ontology OBO files to a tab-delimited text file.
PNNL-Comp-Mass-Spec/OxyDataPlotter
The OxyDataPlotter library includes a WinForms control with a customizable instance of OxyPlot.
PNNL-Comp-Mass-Spec/PeptideListToXML
The PeptideListToXML application reads a tab-delimited text file created by the Peptide Hit Results Processor (PHRP) and creates a PepXML with the appropriate information.
PNNL-Comp-Mass-Spec/Thermo-Peak-Data-Exporter
Extracts peak intensity data from each scan in a Thermo raw file, and writes that data to a tab-delimited text file.
PNNL-Comp-Mass-Spec/VIPER
VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses.
PNNL-Comp-Mass-Spec/Crosstab-Merger
Merge crosstabs (pivot tables) that share the same column layout
PNNL-Comp-Mass-Spec/CSharp-Code-Comment-Sort-Utility
This program sorts documentation comment blocks in C# source code files. Updated files will have comments in the order Summary, Remarks, Parameters, and Returns.
PNNL-Comp-Mass-Spec/File-Comparison-Sampler
The File Comparison Sampler console application compares two or more files to check whether the start of the files match, the end of the files match, and selected sections inside the files also match. It is useful for comparing large files without reading the entire file. It also supports comparison of files in two directories.
PNNL-Comp-Mass-Spec/File-Content-Updater
Replaces text in files, using a text file with a list of search / replace values
PNNL-Comp-Mass-Spec/Interference-Detection
Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).
PNNL-Comp-Mass-Spec/metaPro
Workflow for meta-proteomics analysis
PNNL-Comp-Mass-Spec/MSBuild-Multi-Project-Builder
The MSBuild Multi Project Builder compiles a list of Visual Studio solutions using MSBuild. Following each compile, files can optionally be copied from the output directory to a target directory. Batch files can also optionally be called.
PNNL-Comp-Mass-Spec/MSGFPlus_MASIC_Toolbox
DataProcessing toolbox for running MSGF+ and MASIC, then merging the results. Uses Windows batch files to automate the process for a folder of Thermo .Raw files
PNNL-Comp-Mass-Spec/PlexedPiperTestData
Example of processed TMT data. MoTrPAC pilot study.
PNNL-Comp-Mass-Spec/pwiz
The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
PNNL-Comp-Mass-Spec/Sequest-Results-Processor
Extracts peptide identifications from SEQUEST .out files and stores them in synopsis files (_syn.txt) and first hits files (_fht.txt).
PNNL-Comp-Mass-Spec/SMAQC
SMAQC computes quality metrics for a LC-MS/MS dataset. The quality metrics are based on the metrics proposed by Rudnick and Stein, as described in "Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.", Mol Cell Proteomics. 2010 Feb;9(2):225-41.
PNNL-Comp-Mass-Spec/sqlserver2pgsql
Migration tool to convert a Microsoft SQL Server Database into a PostgreSQL database, as automatically as possible