title: Peek a peak: a glance at statistics for quantitative label-free proteomics.
abstract: Today, label-free mass spectrometry methods are frequently used for quantification of proteins and peptides. There have been several proposals of measurable parameters that best reflect quantities, such as peak areas as well as spectral counts. This review provides a systematic overview of the proposed methods. Owing to the shotgun proteomics approach generally used today for label-free mass spectrometry, any quantitative measure in the first place is a measure of peptide quantity. There has been no systematic research on how to best infer protein quantity from its measured peptides' quantities. The way peptide identifications are assembled to protein lists may especially lead to significantly different results in protein quantification. A further focus of this review will thus be the assembly of measured peptide quantities to a protein quantity.
authors.affiliation: Ruhr-Universität Bochum, Zentrum für Klinische Forschung (ZKF 1), Universitätsstrasse 150, 44801 Bochum, Germany. katharina.podwojski@tu-dortmund.de
authors.forename: Katharina
authors.initials: K
authors.lastname: Podwojski
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
authors.forename: Michael
authors.initials: M
authors.lastname: Kohl
authors.forename: Michael
authors.initials: M
authors.lastname: Turewicz
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.forename: Jörg
authors.initials: J
authors.lastname: Rahnenführer
authors.forename: Christian
authors.initials: C
authors.lastname: Stephan
mesh_terms: D000818:Animals; D006801:Humans; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins