A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. MaxQuant is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
Recognizes and quantifies protein in biologic complex samples. Proteome Discoverer covers a wide range of possible proteomic investigations from proteins and peptides identification to post-translational modification. It searches in many databases and several dissociation technics for performing complete studies. This tool automatizes data analyze and allows researchers to represent results thanks to modules like gene ontology (GO) enrichment.
An LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. The XCMS software reads and processes LC/MS data stored in netcdf , mzXML, mzData and mzML files. It provides methods for feature detection, non-linear retention time alignment, visualization, relative quantization and statistics. XCMS is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples. XCMS is freely available under an open-source license.
A tool for quantifying ratios of differentially labeled proteins. XPRESS calculates the relative abundance of proteins, such as those obtained from an ICAT-reagent labeled experiment, by reconstructing the light and heavy elution profiles of the precursor ions and determining the elution areas of each peak. It allows the specification of which residue(s) are labeled (such as cysteines for ICAT) and what the mass difference of the two isotope labels are (such as 8 Da for ICAT).
Allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass accuracy leading to fewer false positive peptide identifications. Algorithms to increase data quality include an MS(3) score for peptide identification and a post-translational modification (PTM) score that determines the probability that a modification such as phosphorylation is placed at a specific residue in an identified peptide. MSQuant supports relative protein quantitation based on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches.
A comprehensive suite to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. With dynamic extracted ion chromatogram plots, the ability to view every MS spectra at any time point and the ability to manually select a peak area, ProteoIQ® provides the ultimate level of control. ProteoIQ® provides a completely customizable interface to support any form of biological annotation. You can easily compare protein quantitative results in relation to biological pathways, protein localization, protein function, or even compare to transcript abundance. Every protein identification in ProteoIQ® can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or even an in-house LIMS.