Engineering topics
Publications and source records attributed to Gibbons, Bryson.
The OMICS group at PNNL has developed a wide range of software utilities over the last 15+ years. These tools are used to manage data files, transform data, visualize data, and automate data processing. The software is distributed on GitHub as open source, typically under the Apache 2.0 license agreement. See https://github.com/PNNL-Comp-Mass-Spec Lipid analysis tool developed by PNNL
The DMS Analysis Tool Manager is a part of PRISM, the Proteomics Research Information and Management System. The analysis manager performs automated processing of available job steps, tracked by the in the DMS_Pipeline database. Plugin DLLs implement the processing details for each analysis tool.
The DMS Capture Task Manager is a part of PRISM, the Proteomics Research Information and Management System. The capture manager processes instrument data files, copying them from the instrument to storage servers, validating the data, creating QC graphics, and pushing the data into MyEMSL. Plugin DLLs implement the processing details for each tool.
The DMS Update Manager is used to keep automated processing manager software up-to-date. Although it is part of PRISM (the Proteomics Research Information and Management System), it is a standalone program and does not contact any databases. The program compares the files on a central distribution share to files on the local computer, updating any files that are out of date. It supports rolling back local files to an older version and auto-deleting extra files.
The DeconEngine includes routines for deconvoluting (deisotoping) observed isotopic signatures in mass spectrometry data to detect features.
DeconTools is a software package used for detecting features in MS data by using the isotopic signatures of expected components. The tool uses different algorithms for different parts of the deconvolution process: noise reduction, peak detection, prediction of theoretical isotopic envelope and scoring functions that quantitate the quality of signature observed in the data.
InfernoRDN can perform various downstream analyses on large scale datasets from proteomics and microarrays.
The Informed Proteomics project includes algorithms for proteomic mass spectrometry data analysis. Although the back-end data access and some of the scoring routines are general purpose, this repository is currently maintained for top down MS/MS datasets.
The LC-IMS-MS Feature Finder finds LC-IMS-MS features and conformers using deisotoped features from DeconTools.
LCMS raw data and MSGF+ results viewer. LcmsSpectator is a standalone Windows graphical user interface tool for viewing LC-MS data and identifications.
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)
The MS File Info Scanner can be used to scan a series of MS data files (or data folders) and extract 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.
Used to generate an Accurate Mass and Time tag database from local MS/MS search engine results (from SEQUEST, X!Tandem, or MSGF+)
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)
Finds 3D XIC features across LC, m/z, and drift time dimensions
Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.