Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource
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59 BASIC BIOLOGICAL SCIENCES↗
Engineering topics
Fujimoto, Grant
Publications and source records attributed to Fujimoto, Grant.
DeconTools
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.
Crowell, Kevin↗
Informed Proteomics
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.
Fujimoto, Grant↗
LIQUID
LIQUID is a software tool for identifying lipids in LC-MS/MS-based lipidomics data. It is described in publication LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data (doi: 10.1093/bioinformatics/btx046). LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.
Payne, Sam↗
MTDB-Creator
Used to generate an Accurate Mass and Time tag database from local MS/MS search engine results (from SEQUEST, X!Tandem, or MSGF+)
Monroe, Matthew↗
PNNL 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.
Wilkins, Christopher↗
Population Variation Plug-In
A Population Variation plug-in for the Skyline software program that can assist researchers in determining whether their target peptides have known mutations in the general human population.
Fujimoto, Grant↗