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A mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute Quantification (iTRAQ), have been added in this version, including a reporter ion impurity correction, a reporter ion intensity threshold filter and an option for weighted normalization to correct mixing errors. TMT/iTRAQ analysis can be performed on experiments using HCD (High Energy Collision Dissociation) only, CID (Collision Induced Dissociation)/HCD (High Energy Collision Dissociation) dual scans or HCD triple-stage mass spectrometry data. To improve measurement accuracy, we implemented weighted normalization, multiple tandem spectral approach, impurity correction and dynamic intensity threshold features.
A fully automated tool for multiplexed iTRAQ-based quantitation in protein profiling, which is designed as a generic platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. Experiment results demonstrate the high accuracy, full automation, and high-throughput capability of Multi-Q as a large-scale quantitative proteomics tool. These features allow rapid interpretation of output from large proteomic datasets without the need for manual validation.
Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed and accuracy of the database search. Each protein obtains a score by adding its three highest peptide CAA scores, and the protein feature of a peptide is the maximum score of the proteins containing this peptide. PEAKS also provides a user-friendly interface to show each resultant peptide spectrum match from de novo sequencing.
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.
ITMSQ / Isobaric Tandem MS Quantification
A quantitative software tool to improve N- and C-terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. ITMSQ provides an accurate and reliable quantitative solution for N- and C-terminal fragment ion pairs based isobaric MS2 quantitative methods.
An enhanced proteomic result reporting tool for MaxQuant, which is widely used in various types of proteomic studies such as in peptide identification, modification assignment, isotope labelling quantification and label-free quantification. MaxReport can automatically optimize and organize the results of MaxQuant. MaxReport also provides additional functions including generating visualization figures and exporting integrated results for users who are not familiar with bioinformatics to save time in comprehending and interpreting the results.
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.
Scaffold Q+
Allows quantitation of complex tandem mass spectrometry (MS/MS) proteomics experiments. Scaffold Q+ calculate and display relative protein expression levels in a sample determined by tandem mass spectrometry of iTRAQ- or TMT-labeled proteins and precursor intensity quantitation. The software also enables evaluation of population differences across experiments and statistical probabilities with built-in algorithms, simultaneous comparison of multiple population tests simultaneously and combination of multiple quantitative experiments.
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