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Mass spectrometry‐based absolute protein quantification: PSAQ ™ strategy makes use of “noncanonical” proteotypic peptides
Author(s) -
Jaquinod Michel,
Trauchessec Mathieu,
Huillet Céline,
Louwagie Mathilde,
Lebert Dorothée,
Picard Guillaume,
Adrait Annie,
Dupuis Alain,
Garin Jérôme,
Brun Virginie,
Bruley Christophe
Publication year - 2012
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100538
Subject(s) - isotope dilution , chemistry , isobaric labeling , mass spectrometry , quantitative proteomics , label free quantification , peptide , chromatography , tandem mass spectrometry , tandem mass tag , proteomics , biochemistry , protein mass spectrometry , gene
Absolute quantification of proteins using isotope dilution mass spectrometry requires the selection of proteotypic peptides. When choosing these peptides, a certain number of rules must be respected. Several of these were established to safeguard against quantification errors resulting from the isotopically labeled standard peptides not behaving in the same way as the peptides to be quantified. Of all absolute quantification methods using isotope dilution, P rotein S tandard for A bsolute Q uantification ( PSAQ TM ) offers the maximal protein sequence coverage. In the present study, we show that the PSAQ method presents a previously unreported advantage for protein quantification as it makes use of M et/ C ys‐containing peptides and peptides‐containing miscleavages in addition to proteotypic peptides. By increasing the total number of peptides that can be considered, robustness of quantification is improved, paving the way for a facilitated quantification of low abundant and/or low‐molecular‐weight proteins.