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Quantitative proteomics using uniform N-15-labeling, MASCOT, and the trans-proteomic pipeline

Palmblad, M., Bindschedler, L.V. and Cramer, R. (2007) Quantitative proteomics using uniform N-15-labeling, MASCOT, and the trans-proteomic pipeline. Proteomics, 7 (19). pp. 3462-3469. ISSN 1615-9853

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To link to this article DOI: 10.1002/pmic.200700180

Abstract/Summary

Stable isotope labeling combined with MS is a powerful method for measuring relative protein abundances, for instance, by differential metabolic labeling of some or all amino acids with N-14 and N-15 in cell culture or hydroponic media. These and most other types of quantitative proteomics experiments using high-throughput technologies, such as LC-MS/MS, generate large amounts of raw MS data. This data needs to be processed efficiently and automatically, from the mass spectrometer to statistically evaluated protein identifications and abundance ratios. This paper describes in detail an approach to the automated analysis of Uniformly N-14/N-15-labeled proteins using MASCOT peptide identification in conjunction with the trans-proteomic pipeline (TPP) and a few scripts to integrate the analysis workflow. Two large proteomic datasets from uniformly labeled Arabidopsis thaliana were used to illustrate the analysis pipeline. The pipeline can be fully automated and uses only common or freely available software.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences
Faculty of Life Sciences > School of Chemistry, Food and Pharmacy > Department of Chemistry
Interdisciplinary centres and themes > Chemical Analysis Facility (CAF)
ID Code:11545
Uncontrolled Keywords:arabidopsis, bioinformatics, liquid chromatography-tandem mass spectrometry, quantitative analysis , CODED AFFINITY TAGS, MASS-SPECTROMETRY, LIQUID-CHROMATOGRAPHY, SHOTGUN PROTEOMICS, PROTEIN ABUNDANCE, ARABIDOPSIS, COMPLEX, STRESS, MANIPULATION, RESISTANCE

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