title: Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
abstract: Mass spectrometry (MS)-based shotgun proteomics allows protein identifications even in complex biological samples. Protein abundances can then be estimated from the counts of tandem MS (MS/MS) spectra attributable to each protein, provided one accounts for differential MS detectability of contributing peptides. We developed a method, APEX, which calculates Absolute Protein EXpression levels based upon learned correction factors, MS/MS spectral counts and each protein's probability of correct identification. This protocol describes APEX-based calculations in three parts. (i) Using training data, peptide sequences and their sequence properties, a model is built to estimate MS detectability (O(i)) for any given protein. (ii) Absolute protein abundances are calculated from spectral counts, identification probabilities and the learned O(i)-values. (iii) Simple statistics allow calculation of differential expression in two distinct biological samples, i.e., measuring relative protein abundances. APEX-based protein abundances span 3-4 orders of magnitude and are applicable to mixtures of 100s to 1,000s of proteins.
authors.affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, MBB 3.210, Austin, Texas 78712, USA. cvogel@mail.utexas.edu
authors.forename: Christine
authors.initials: C
authors.lastname: Vogel
authors.forename: Edward M
authors.initials: EM
authors.lastname: Marcotte
mesh_terms: D008957:Models, Genetic; D011506:Proteins / Q000032:analysis* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins