Allows users to convert Mascot compatible files into SAM files. Samifier is a part of the PG Nexus pipeline and is available as both a standalone application and through the Galaxy platform. The software provides outputs that can be displayed in a genomics viewer by translating peptides arising from tandem mass spectrometry (MS/MS) analysis of complex proteomics samples while allowing configuration of a peptide confidence threshold score.
Presents the results from ProMex and MSPathFinder in a format that allows quick manual evaluation of critical attributes for high-confidence proteoform identifications. LcMsSpectator is a standalone Windows graphical user interface (GUI) tool for viewing liquid chromatography-mass spectrometry (LC-MS) data and identifications. It takes a single or multiple Thermo raw files (*.raw) and shows MS and MS/MS spectra as well as precursor and product ion chromatograms as resizable, floatable tabbed-documents. Identification and target files can also be loaded to show the spectral and chromatographic evidence.
Simplifies the integration of metadata in the experimental workflow and fills the gap between the ISA-compliant data collection and curation and the data analysis phases. Risa provides generic methods to parse and save Investigations, Studies and Assay (ISA)-Tab metadata. It offers functionality to build specific, metadata informed objects, readily available for subsequent analysis. This tool can be useful in mass spectrometry and DNA microarray.
Provides a tool for mass spectrometry data visualization, annotation, and notebooking. mzStudio allows researchers to corroborate peptide-spectral-matches and associated quantitative measures across large, multidimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) data sets. Instrument platforms and search engines are also concerned. This software is appropriate to assist for describing novel modifications or surprising gas phase fragmentation behavior.
Offers a platform dedicated to proteomics data annotation and interpretation. ProteoRE includes multiple panels for: (i) data managing, supplying filters, a converter and a JVenn diagram generator; (ii) protein list annotating; (iii) annotation retrieving from the human protein atlas (HPA) database; (iv) functional analyzing, including two modules for enrichment analysis and one to generate statistics dealing with functional profiles and (v) pathway analyzing.
Reads the contents of a tab-delimited peptide hit results file (e.g. from Sequest, XTandem, Inspect, or MSGF+). MASIC Results Merger is a package that generates input data with the corresponding MASIC results files, appending the relevant MASIC stats for each peptide hit result.
Assists users to analyze proteomic data. PaDuA includes several modules allowing different actions: (1) reading and writing both MaxQuant and Perseus format files; (2) filtering data by quality and features; (3) incorporating experimental design, labels to index, expand-side-table; (4) performing normalisation methods; (5) adding annotation metadata for quantified proteins; or (6) performing simple analyses such as column correlations.
Generates an Accurate Mass and Time tag database (Microsoft Access format) from local MS/MS search engine results from either SEQUEST or X!Tandem. MTDB Creator can act as input to VIPER and MultiAlign for matching high resolution LC-MS features to peptides.
Converts Agilent MassHunter format (.d directories) to mzXML. Trapper is a package for Windows that relies on the MassHunter Data Accquisition Component (MHDAC), which is included with the trapper installer by kind permission of Agilent. It allows to use data files, without requiring installation of the full MassHunter application. This program is no longer supported.
Consists of a series of Windows batch files for the automated analysis of Thermo .Raw files. MSGFPlus/MASIC Data Processing toolbox is an ensemble of software for running MSGF+ and MASIC. Following the analysis, the results are merged into a single, master result file.
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