MassChroQ Mass Chromatogram Quantification software
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chromatogram quantification

MassChroQ Description

MassChroQ is a specialized and versatile instrument that performs quantifications on the data obtained from Liquid Chromatography-Mass Spectrometry (LC-MS) techniques. MassChroQ can also be used to perform alignments, XIC extractions and peak detections. Moreover, MassChroQ can be used to: · analyze data obtained from both high and low resolution spectrometer systems; · analyze label-free as well as isotopic labeled data (e.g. SILAC, ICAT, N-15, C-13, etc.); · time-efficiently process a large amount of differently analyzed samples in one shot (by grouping similar samples and offering the possibility to parametrize the analysis of each group). · take into account complex data treatments as peptide or protein fractionation prior to LC-MS analysis (SCX, SDS-PAGE, etc.); Main features: Parsing of mzXML and mzML LC/MS data formats. Quantification of all the identified peptides of the samples and/or a given list of mass over charge (m/z) values and/or a given list of (m/z, retention time) pairs of values. The identified peptides can be automatically integrated into MassChroQ's analysis by using our X!Tandem pipeline (which performs identification and exports the results in masschroqML format) or via TSV (Tab Separated Values) files containing the identification results obtained from other identification software. Two alignment methods are available: the third-party OBI-Warp alignment based on MS level 1 data is integrated in MassChroQ, and the in-house developed MS2 alignment based on MS level 2 information. The quantification in MassChroQ is performed on XICs (eXtracted Ion Chromatograms): after XIC extraction and filtering, peaks are detected on them by using morphological transforms (see the user manual for details). Peak areas (i.e. quantification value) and boundaries are then computed. Peak matching is performed (after alignment if any) as follows: a detected peak is assigned to an identified peptide if and only if the (aligned) retention time of this peptide is located within the peak boundaries. Peak matching in MassChroQ can be performed in two rounds: a first one during quantification, and once quantification is finished, the user can perform a second, improved peak matching round, taking into account the retention times of the previously matched peaks. Various XIC filters are available : moving median/mean filters to smooth the signal, background and baseline noise removal filters, anti-spike filter to remove spikes caused by some high resolution spectrometers, morphological filters, etc. The user can export results in TSV, gnumeric, xhtml and masschroqML formats. They are ready for automatical use in statistical software (like R) or for manual/visual exploration. Evaluation of MassChroQ on complex label-free data obtained from both low and high resolution mass spectrometers allowed the measurement of low CVs for technical reproducibility (1.4%) and high coefficients of correlation to protein quantity (0.98)

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