Computational Mass Spectrometry @ Pacific Northwest National Laboratory

  • MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis. The SICs are generated using the LC-MS data, then each SIC is processed using a peak finding algorithm to characterize the chromatographic peaks, providing peak statistics including elution time of the peak apex, peak ar…

    Visual Basic Updated Jan 21, 2017
  • Utility for manually and automatically adding datasets to DMS

    C# Updated Jan 21, 2017
  • PRISM Data Management System database schema

    SQLPL 2 Updated Jan 21, 2017
  • 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.

    C# Updated Jan 19, 2017
  • 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)

    C# 1 1 Updated Jan 17, 2017
  • The DeconEngine includes routines for deconvoluting (deisotoping) observed isotopic signatures in mass spectrometry data to detect features.

    C++ Updated Jan 17, 2017
  • .NET DLL wrapper for Thermo's MS File Reader, which is accessible by creating an account at https://thermo.flexnetoperations.com/control/thmo/login then logging in and choosing "Utility Software"

    C# Updated Jan 17, 2017
  • DMS Website

    PHP Updated Jan 17, 2017
  • DMS Analysis Tool Manager

    Visual Basic Updated Jan 16, 2017
  • PRISM Mass and Time Tag System database schema

    SQLPL 1 1 Updated Jan 14, 2017
  • The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.

    Visual Basic Updated Jan 14, 2017
  • DMS Capture Task Manager

    C# Updated Jan 14, 2017
  • BioPython scripts for conversion of GBK files or DNA-based FASTA files to protein FASTA files

    Python Updated Jan 13, 2017
  • DeconMSn converts mass spectrometry instrument data to text files, including determining the charge state for each parent ion.

    C++ Updated Jan 12, 2017
  • Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data

    C# 1 1 Updated Jan 11, 2017
  • SDK for controlling the Adaptable Multiple Power Supplies (AMPS boxes)

    C# 2 2 Updated Jan 5, 2017
  • The Mage suite of tools provide access to DMS files and metadata.

    C# Updated Dec 23, 2016
  • Used to de-isotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.

    C# 6 Updated Dec 16, 2016
  • 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)

    C# 1 1 Updated Dec 15, 2016
  • Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.

    C# Updated Dec 8, 2016
  • Lipid analysis tool developed by PNNL

    C# Updated Dec 6, 2016
  • 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.

    C# Updated Nov 24, 2016
  • The Peptide Hit Results Processor can be used to convert an X!Tandem results file (XML format) or a SEQUEST Synopsis/First Hits file to a series of tab-delimited text files summarizing the results. The program also supports MSGF+ (aka MS-GFDB). When parsing X!Tandem data, the program will insert modification symbols into the peptide sequences fo…

    Visual Basic Updated Nov 23, 2016
  • C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.

    C# Updated Nov 18, 2016
  • C# classes that can be used to interface with the ProteoWizard libraries

    C# Updated Nov 18, 2016
  • DataImportManager (DIM)

    Visual Basic Updated Nov 18, 2016
  • Performs validation, transformation, and in-silico digestion of text files containing protein or peptide sequences (FASTA format or delimited text)

    Visual Basic Updated Nov 14, 2016
  • 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.

    Visual Basic Updated Nov 14, 2016
  • LCMS raw data and MSGF+ results viewer

    C# Updated Nov 11, 2016
  • DMS EMail Manager

    Visual Basic Updated Nov 11, 2016