Journal ArticleDOI
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry.
TLDR
The utility of the ASAPRatio program was clearly demonstrated by its speed and the accuracy of the generated protein abundance ratios and by its capability to identify specific core components of the RNA polymerase II transcription complex within a high background of copurifying proteins.Abstract:
We describe an algorithm for the automated statistical analysis of protein abundance ratios (ASAPRatio) of proteins contained in two samples. Proteins are labeled with distinct stable-isotope tags and fragmented, and the tagged peptide fragments are separated by liquid chromatography (LC) and analyzed by electrospray ionization (ESI) tandem mass spectrometry (MS/MS). The algorithm utilizes the signals recorded for the different isotopic forms of peptides of identical sequence and numerical and statistical methods, such as Savitzky-Golay smoothing filters, statistics for weighted samples, and Dixon's test for outliers, to evaluate protein abundance ratios and their associated errors. The algorithm also provides a statistical assessment to distinguish proteins of significant abundance changes from a population of proteins of unchanged abundance. To evaluate its performance, two sets of LC-ESI-MS/MS data were analyzed by the ASAPRatio algorithm without human intervention, and the data were related to the expected and manually validated values. The utility of the ASAPRatio program was clearly demonstrated by its speed and the accuracy of the generated protein abundance ratios and by its capability to identify specific core components of the RNA polymerase II transcription complex within a high background of copurifying proteins.read more
Citations
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Journal ArticleDOI
3DSpectra: A 3-dimensional quantification algorithm for LC-MS labeled profile data.
TL;DR: The 3DSpectra software showed significantly higher linearity, quantification accuracy, and precision than did ASAPRatio in this real use case simulation where the true ratios are known, and it also achieved wider peptide coverage and dynamic range.
Ozone- and ultraviolet radiation-induced signalling in plants
TL;DR: Results indicate that the ozoneand hydrogen peroxide-induced activation of MAPK 4 6 is signalling through a cognate MAPKK(s) that is sensitive to PD98059, whereas UVC may utilize a MAPKK which is insensitive to PD 98059.
Proceedings ArticleDOI
QuantWiz: A Parallel Software Package for LC-MS-based Label-Free Protein Quantification
TL;DR: This paper described the framework design and prototype development of this new domestic parallel software package called QuantWiz for high performance Liquid Chromatography (short for LC)-MS-based label-free protein quantification, and implemented the parallelization version.
Book ChapterDOI
Analysis of Labeled Quantitative Mass Spectrometry Proteomics Data
TL;DR: The quantification of proteins in complex samples, the monitoring of specific post-translational modification (PTM) changes, and the identification of biomarkers pose challenges to the experimentalists and to the algorithmic and statistical techniques applied.
References
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Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels
Andrej Shevchenko,O. N. Jensen,Alexandre V. Podtelejnikov,Sagliocco F,Matthias Wilm,Ole Vorm,Peter Mortensen,Boucherie H,Matthias Mann +8 more
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A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
Blagoy Blagoev,Irina Kratchmarova,Shao En Ong,Mogens Brøndsted Nielsen,Leonard J. Foster,Matthias Mann +5 more
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