2011/11/21 by Thomas I. Milac, Milac, Thomas I., Timothy W. Randolph +3
Biochemistry, Genetics and Molecular Biology · Chemistry · Mathematics · #Advanced Proteomics Techniques and Applications #Applications (stat.AP) #FOS: Biological sciences #FOS: Computer and information sciences #Mass Spectrometry Techniques and Applications #Metabolomics and Mass Spectrometry Studies #Quantitative Methods (q-bio.QM) #q-bio.QM #stat.AP
paper · pdf · doi:10.48550/arxiv.1111.4721
12 pages, 10 figures
arxiv created 2011/11/21 · openalex publication_date 2011/11/21 · arxiv updated 2015/03/19 · openalex created_date 2019/06/27 · openalex updated_date 2026/07/28
In comparative proteomics studies, LC-MS/MS data is generally quantified using one or both of two measures: the spectral count, derived from the identification of MS/MS spectra, or some measure of ion abundance derived from the LC-MS data. Here we contrast the performance of these measures and show that ion abundance is the more sensitive. We also examine how the conclusions of a comparative analysis are influenced by the manner in which the LC-MS/MS data is `rolled up' to the protein level, and show that divergent conclusions obtained using different rollups can be informative. Our analysis is based on two publicly available reference data sets, BIATECH-54 and CPTAC, which were developed for the purpose of assessing methods used in label-free differential proteomic studies. We find that the use of the ion abundance measure reveals properties of both data sets not readily apparent using the spectral count.