Quantitative analysis of SILAC data sets using spectral counting. Proteomics 2010 Apr;10(7):1408-15
Date
01/28/2010Pubmed ID
20104619Pubmed Central ID
PMC4326228DOI
10.1002/pmic.200900684Scopus ID
2-s2.0-77950651307 (requires institutional sign-in at Scopus site) 10 CitationsAbstract
We report a new quantitative proteomics approach that combines the best aspects of stable isotope labeling of amino acids in cell culture (SILAC) labeling and spectral counting. The SILAC peptide count ratio analysis (SPeCtRA, http://proteomics.mcw.edu/visualize) method relies on MS(2) spectra rather than ion chromatograms for quantitation and therefore does not require the use of high mass accuracy mass spectrometers. The inclusion of a stable isotope label allows the samples to be combined before sample preparation and analysis, thus avoiding many of the sources of variability that can plague spectral counting. To validate the SPeCtRA method, we have analyzed samples constructed with known ratios of protein abundance. Finally, we used SPeCtRA to compare endothelial cell protein abundances between high (20 mM) and low (11 mM) glucose culture conditions. Our results demonstrate that SPeCtRA is a protein quantification technique that is accurate and sensitive as well as easy to automate and apply to high-throughput analysis of complex biological samples.
Author List
Parker SJ, Halligan BD, Greene ASMESH terms used to index this publication - Major topics in bold
Amino AcidsAnimals
Cells, Cultured
Databases, Protein
Endothelial Cells
Glucose
Isotope Labeling
Male
Proteomics
Rats
Rats, Sprague-Dawley
Reproducibility of Results
Tandem Mass Spectrometry
