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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Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.
TL;DR: A review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing is provided.
Journal ArticleDOI
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry.
W. Andy Tao,W. Andy Tao,Bernd Wollscheid,Robert V. O’Brien,Jimmy K. Eng,Xiao-Jun Li,Bernd Bodenmiller,Julian D. Watts,Leroy Hood,Ruedi Aebersold,Ruedi Aebersold +10 more
TL;DR: A robust and general method is presented for the identification and relative quantification of phosphorylation sites in complex protein mixtures based on a new chemical derivatization strategy using a dendrimer as a soluble polymer support and tandem mass spectrometry (MS/MS).
Journal ArticleDOI
TOPP---the OpenMS proteomics pipeline
Oliver Kohlbacher,Knut Reinert,Clemens Gröpl,Eva Lange,Nico Pfeifer,Ole Schulz-Trieglaff,Marc Sturm +6 more
TL;DR: The basic concepts and the current abilities of TOPP are described and illustrated in the context of two example applications: the identification of peptides from a raw dataset through database search and the complex analysis of a standard addition experiment for the absolute quantitation of biomarkers.
Journal ArticleDOI
Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism
Stefan Schmollinger,Timo Mühlhaus,Nanette R. Boyle,Ian K. Blaby,David Casero,Tabea Mettler,Jeffrey L. Moseley,Janette Kropat,Frederik Sommer,Daniela Strenkert,Dorothea Hemme,Matteo Pellegrini,Arthur R. Grossman,Mark Stitt,Michael Schroda,Sabeeha S. Merchant +15 more
TL;DR: Comparison of the N-replete versus N-deplete proteome indicated that abundant proteins with a high N content are reduced in N-starved cells, while the proteins that are increased have lower than average N contents, suggesting an approach for engineering increased N-use efficiency.
Journal ArticleDOI
Proteomic Identification of a Stress Protein, Mortalin/mthsp70/GRP75 Relevance To Parkinson Disease
TL;DR: Manipulations of mortalin level in dopaminergic neurons resulted in significant changes in sensitivity to PD phenotypes via pathways involving mitochondrial and proteasomal function as well as oxidative stress.
References
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Journal ArticleDOI
Probability-based protein identification by searching sequence databases using mass spectrometry data.
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
Journal ArticleDOI
A statistical model for identifying proteins by tandem mass spectrometry.
TL;DR: A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample, and it is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications.
Journal ArticleDOI
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Trey Ideker,Vesteinn Thorsson,Jeffrey A. Ranish,Rowan H. Christmas,Jeremy Buhler,Jimmy K. Eng,Roger E. Bumgarner,David R. Goodlett,Ruedi Aebersold,Leroy Hood +9 more
TL;DR: An integrated approach to build, test, and refine a model of a cellular pathway, in which perturbations to critical pathway components are analyzed using DNA microarrays, quantitative proteomics, and databases of known physical interactions, suggests hypotheses about the regulation of galactose utilization and physical interactions between this and a variety of other metabolic pathways.
Journal ArticleDOI
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
TL;DR: This study establishes that mass spectrometry provides the required throughput, the certainty of identification, and the general applicability to serve as the method of choice to connect genome and proteome.
Journal ArticleDOI
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
TL;DR: Stable isotopic amino acids in cell culture is employed to differentially label proteins in EGF-stimulated versus unstimulated cells and SILAC combined with modification-based affinity purification is a useful approach to detect specific and functional protein-protein interactions.