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…
Utility for manually and automatically adding datasets to DMS
PRISM Data Management System database schema
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.
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)
The DeconEngine includes routines for deconvoluting (deisotoping) observed isotopic signatures in mass spectrometry data to detect features.
.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"
DMS Analysis Tool Manager
PRISM Mass and Time Tag System database schema
The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.
DMS Capture Task Manager
BioPython scripts for conversion of GBK files or DNA-based FASTA files to protein FASTA files
DeconMSn converts mass spectrometry instrument data to text files, including determining the charge state for each parent ion.
Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
SDK for controlling the Adaptable Multiple Power Supplies (AMPS boxes)
The Mage suite of tools provide access to DMS files and metadata.
Used to de-isotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
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)
Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.
Lipid analysis tool developed by PNNL
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.
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…
C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.
C# classes that can be used to interface with the ProteoWizard libraries
Performs validation, transformation, and in-silico digestion of text files containing protein or peptide sequences (FASTA format or delimited text)
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.
LCMS raw data and MSGF+ results viewer
DMS EMail Manager