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Thermo-Raw-File-Reader
.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher ScientificInformed-Proteomics
Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry dataLIQUID
Software tool for identifying lipids in LC-MS/MS-based lipidomics dataDeconTools
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).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.Molecular-Weight-Calculator-VB6
Molecular Weight Calculator (MWTWin): Graphical program written in VB6 with numerous mass calculation utilities.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.AutoCCS
Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometryLCMS-Spectator
LCMS raw data and MS-GF+ results viewerFormultitude
Software for the assignment of low weight molecular formulas from high-resolution mass spectra.proteomics-data-analysis-tutorial
A comprehensive tutorial for proteomics data analysis in R that utilizes packages developed by researchers at PNNL and from Bioconductor.Venn-Diagram-Plotter
The Venn Diagram Plotter draws correctly proportioned and positioned two and three circle Venn diagrams (aka Euler diagrams) whose colors can be customized and the diagrams copied to the clipboard or saved to disk.protein-coverage-summarizer
Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.Mzid-To-Tsv-Converter
Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.Protein-Digestion-Simulator
Performs validation, transformation, and in-silico digestion of text files containing protein or peptide sequences (FASTA format or delimited text)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.exeuimfpy
UIMF python libraryThermo-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.InfernoRDN
InfernoRDN can perform various downstream analyses on large scale datasets from proteomics and microarraysRomicsProcessor
R package that provides a structured R object to store and analyze omics dataPSI-Interface
C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.TopPICR
R package for processing results from TopPIC, including resolving ambiguity in proteoform identificationLCMSNet
LCMSNet software for instrument controlDBSchema_PgSQL_DMS
PRISM Data Management System PostgreSQL database schemaSimELIT
multi-physics and multi-scale simulation software for mass spectrometryUniprot-DAT-File-Parser
This program can read a Uniprot .Dat file and parse out the information for each entry, creating a tab delimited text file or a FASTA file.AqMD3-Acquisition-Console
Acquisition software for the Acqiris SA220P digitizer cardChemstationMSFileReader
Allows for reading Agilent Chemstation .D folders using Dot.NETDMS-Analysis-Manager
DMS Analysis Tool ManagerDBSchema_DMS
PRISM Data Management System database schemaMS-Data-File-Reader
A VB.NET DLL that can read mass spectrometry data from four file formats: mzXML, mzData, concatenated .dta files (_dta.txt), and Mascot Generic Format files (.mgf)DBSchema_MTS
PRISM Mass and Time Tag System database schemaMultiAlign
Aligns multiple LC-MS datasets to one another after which LC-MS features can be matched to a database of peptides (typically an AMT tag database)Proteowizard-Wrapper
C# classes that can be used to interface with the ProteoWizard librariesKaiko
deep learning-based de novo peptide sequencing toolMetabolomicsCCS
This is a the code and data for a website created to display collision cross section data for metabolites and small moleculesFasta-File-Splitter
The FASTA File Splitter program can be used to split apart a protein FASTA file into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.SQLServer-Stored-Procedure-Converter
Converts SQL Server stored procedures to PostgreSQL compatible stored proceduresBP-Quant
MyEMSL-Reader
MyEMSL ReaderMzidMerger
Merges split-FASTA MS-GF+ search result .mzid files.Q4SRM
Q4SRM: Quality assessment for QQQ SRMPRISM-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.MyEMSL-MTS-File-Cache-Manager
MTS manager for retrieving files from MyEMSLBrukerDataReader
Bruker data readerStep-Field-CCS
Step field collisional cross section (CCS) calculationMSCC
Multidimensional Stoichiometric Compound ClassificationDeepKS
bsf-py
Python wrapper for Blazing Signature FilterAmpsSDK
SDK for controlling the Adaptable Multiple Power Supplies (AMPS boxes)LipidMiniOn
Shiny interface for the Lipid Mining and Ontology (Lipid Mini-On) tool, which uses the Rodin R packageTissue_Classification
Multidimensional-Peak-Finding
Finds 3D XIC features across LC, m/z, and drift time dimensionsIMS-Drift-Time-Aligner
Processes IMS data in a UIMF file to align all frames to a base frame, adjusting the observed drift times of each frame to align with the base frame.IMS-Informed-Library
ImsInformed is a .NET class library that provides target identification workflows for peptides and metabolites alike in IMS experiment runs.GlyQ-IQ
GlyQ-IQ is a program that performs a targeted, chromatographic centric search of mass spectral data for glycans.BioPython_Scripts
BioPython scripts for conversion of GBK files or DNA-based FASTA files to protein FASTA filesOBO-Data-Converter
Utility for converting ontology OBO files to a tab-delimited text file.LINCS-Finder
a web app to find the most interesting signatures from LINCS L1000DMS-Website
DMS WebsitePHRP
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.Buzzard
Utility for manually and automatically adding datasets to DMSRodin
R package used by Lipid Mini-On to create ontology bins and perform lipid enrichment analysis.UIMF-Viewer
Visualization software for IMS data stored in a UIMF fileFasta-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.MetaboliteValidation
This is a simple c# console program to validate the data from Erin's Metabolite ccsDL-Batch-Correction
LIPID-Split
Splits lipid annotation names by fatty acid. Adds total number of chain carbons and double bonds as new columns.CRNT4SBML
Uses chemical reaction network theory to evaluate whether a system encoded by SBML could be bistablePNNL.DMS.utils
Tools to interface with PNNL's DMS in RThermo-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.OxyDataPlotter
The OxyDataPlotter library includes a WinForms control with a customizable instance of OxyPlot.LC-IMS-MS-Feature-Finder
Finds LC-IMS-MS features using deisotoped features from DeconToolsValidate-Fasta-File
Parses a FASTA file (with protein name and sequence information) to check for valid text. Also returns protein and residue stats.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)proteinisletplotter
PIXIE
ImsMetabolitesFinder searches for the presence of a target molecule in a UIMF file. The target mobility(K0) and cross sectional area(A) can be computed with varying drift tube voltagesBSF_publication
All the data and materials for the publication about the Blazing Signature FilterSipper
Used to automatically detect and quantify partially labeled C13 peptides in a mass spectrometry dataset.Kaiko_Publication
all the materials for the publication about the Kaikobsf-core
C++ library of Blazing Signature FilterVIPER
VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses.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.LipidFDR
Python scripts of SVM model training and testing used in a publication entitled 'A generalizable method for false-discovery rate estimation in mass spectrometry-based lipidomics'PepAligner
The PepAligner program can read a file containing peptides and align them to a file of protein sequences (.Fasta or delimited text) using Smith-Waterman alignment.R_skills_assessment
Atreyu
Ion mobility mass spectrometry data viewer and extractor, targeted toward PNNL's UIMF filesProtein-Sequence-Motif-Extractor
Reads a FASTA file or tab delimited file containing protein sequences, then looks for the specified motif in each protein sequence. Results are stored in a new file containing the regions of the protein that contain the specified motif.PNNL-Comp-Mass-Spec.github.io
Markdown files displayed at https://pnnl-comp-mass-spec.github.io/APE-DLL
The APE DLL is a library of methods used by the APE GUI to apply a series of data transformations to data stored in a SQLite database. The set of transformations is called a Workflow, and is composed of sequential steps to apply.DataFilter-DLL
Butterworth filter, Moving Window Average filter, and Savitzky Golay filterMASIC-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.SAIS-CSharp
Suffix array, induced sorting library. Source from https://sites.google.com/site/yuta256/sais, with updated project and framework configurationPeptide-Fragmentation-Modeller
The Peptide Fragmentation Modeller is a command-line utility reads that reads in a text file of peptide sequences and generates the theoretical fragmentation pattern for each, outputting the results in a single concatenated DTA file, or in separate .Dta files. The ion intensity values are not predicted values; instead, b, c, y, and z ions are assigned an intensity of 100; while a ions and neutral loss ions receive an intensity of 20.MotrpacRatTrainingPhysiologyData
Data and analysis results for the MoTrPAC PASS1B rat physiology manuscriptPNNL-Biodiversity-Library-Plugin
The PNNL Biodiversity Plugin is a software tool for Skyline and is designed to allow pathway-centric browsing of peptides previously identified by LC-MS/MS. The plugin is designed to assist in SRM assay design or DIA data analysis. Users select an organism and biological pathway of interest, then the plugin shows information about the associated peptides. In total the Biodiversity Library catalogs MS/MS spectra from 2 million peptides and 200,000 proteins from over 118 distict organisms. Users can optionally import peptide data for selected proteins into Skyline to extend their local copy of the Biodiversity Library.PNNL-PreProcessor
Distribution binaries for the PNNL PreProcessorAScore
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.Love Open Source and this site? Check out how you can help us