MS/MS protein identification software, available for Linux and Windows, Phenyx is scallable in terms of computing nodes and supports many input data formats. Search results can be exported from MS Excel to XML formats
henyx enables proteomics scientists to 1) submit MS/MS data and iden...
The Trans-Proteomic Pipeline (TPP) includes all of the steps of the ISB MS/MS analysis pipeline, after the database search. Most users will only need to download the TPP distrubtion.
Computational Proteomics Analysis System. CPAS is a suite of database and analysis tools, originally developed in the FHCRC CPL, that manages proteomics experimental workflows and integrates database search algorithms (X!Tandem, Mascot, and Sequest) and Institute for Systems Biology (IS...
Derived from CPAS. LabKey Server incorporates a robust data pipeline for importing and processing mass spectrometry data from raw and mzXML data files. The pipeline manages the chain of processing steps needed to infer protein identifications and expression levels from the output of a m...
a Java-based, modular software platform for integration, visualization and analysis of complex proteomics mass spectrometry data sets. The software has a graphical user interface and provides access to data produced by data analysis pipelines such as the Trans-Proteomic Pipeline. It bri...
OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL. OpenMS will be compatible with the upcoming Proteomics Standard ...
ProteoWizard is a modular and extensible set of open-source, cross-platform tools and software libraries for proteomics data analysis. The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and perfor...
XCMS is an LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a ...
Mass++ is software for mass spectrometer. The software can read and process various MS data format. Mass++ is a plug-in style software. So users can customize Mass++ depending on their purposes such as addition of new functions and deleting unnecessary functions to increase pefomance wi...
mspire - 'Mass Spectrometry Proteomics in Ruby' is a collection of tools for working with MS proteomics data in ruby. It seeks to provide support for open standards (e.g., parsers for mzData, mzXML, Peptide/Protein Prophet and the TPP) and contribute other useful functionality for worki...
sInspect allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis ...
The Insilicos platform is a flexible, high-throughput system for analysis of biological samples and identification of biomarkers. Uniquely, the Insilicos platform can achieve nearly complete coverage of biomarker proteins in complex samples.
a “simple to use” yet efficient and panoptic software to addresses shotgun proteomic data analysis that was initialy published in BMC Bioinformatics in 2008.
s a single, user-friendly, informatic framework, that is simple to use and fully customizable, for the enabling of LC-MS-based quantitative proteomic workflows of any size, able to guide the user seamlessly from MS data generation, through data processing, visualization, and statistical...
TIQAM (Targeted Identification for Quantitative Analysis by MRM) is developed as a suite of software tools to support targeted indentification and quantification using multiple reaction monitoring (MRM) mass spectum technology. More specifically, TIQAM software provided user friendly in...
PEAKS is a suite of tools, each specifically designed to solve a unique problem. One tool, or a selection of tools from the PEAKS family will suit your environment.
The Rosetta Elucidator® system is a data management and analysis solution for mass spectrometry data, and supports multiple workflows (label-free, SILAC, and shotgun proteomics and metabolomics), data from different instruments, and integration with different search engines for accurate...