Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments

@article{citeulike:1708100, abstract = {Liquid chromatography (LC) coupled to electrospray mass spectrometry (MS) is well established in high-throughput proteomics. The technology enables rapid identification of large numbers of proteins in a relatively short time. Comparative quantification of identified proteins from different samples is often regarded as the next step in proteomics experiments enabling the comparison of protein expression in different proteomes. Differential labeling of samples using stable isotope incorporation or conjugation is commonly used to compare protein levels between samples but these procedures are difficult to carry out in the laboratory and for large numbers of samples. Recently, comparative quantification of label-free LCn-MS proteomics data has emerged as an alternative approach. In this review, we discuss different computational approaches for extracting comparative quantitative information from label-free LCn-MS proteomics data. The procedure for computationally recovering the quantitative information is described. Furthermore, statistical tests used to evaluate the relevance of results will also be discussed. 10.1093/bib/bbm046}, author = {Wong, Jason W. and Sullivan, Matthew J. and Cagney, Gerard }, citeulike-article-id = {1708100}, doi = {10.1093/bib/bbm046}, journal = {Brief Bioinform}, keywords = {bioinformatics, computational, lc-ms, mass-spec, proteomics, quantitation}, month = {September}, pages = {bbm046+}, posted-at = {2008-03-31 00:30:35}, priority = {2}, title = {Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments}, url = {http://dx.doi.org/10.1093/bib/bbm046}, year = {2007} }

TY - JOUR ID - citeulike:1708100 L3 - citeulike-article-id:1708100 TI - Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments JF - Brief Bioinform SP - bbm046 N2 - Liquid chromatography (LC) coupled to electrospray mass spectrometry (MS) is well established in high-throughput proteomics. The technology enables rapid identification of large numbers of proteins in a relatively short time. Comparative quantification of identified proteins from different samples is often regarded as the next step in proteomics experiments enabling the comparison of protein expression in different proteomes. Differential labeling of samples using stable isotope incorporation or conjugation is commonly used to compare protein levels between samples but these procedures are difficult to carry out in the laboratory and for large numbers of samples. Recently, comparative quantification of label-free LCn-MS proteomics data has emerged as an alternative approach. In this review, we discuss different computational approaches for extracting comparative quantitative information from label-free LCn-MS proteomics data. The procedure for computationally recovering the quantitative information is described. Furthermore, statistical tests used to evaluate the relevance of results will also be discussed. 10.1093/bib/bbm046 KW - bioinformatics KW - computational KW - lc-ms KW - mass-spec KW - proteomics KW - quantitation AU - Wong, Jason AU - Sullivan, Matthew AU - Cagney, Gerard PY - 2007/09/28/ UR - http://dx.doi.org/10.1093/bib/bbm046 ER -