title: Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of "noncanonical" proteotypic peptides.
abstract: 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, Protein Standard for Absolute Quantification (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 Met/Cys-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.
authors.affiliation: CEA, IRTSV, Biologie à Grande Echelle, Grenoble, France. jaquinod@cea.fr
authors.forename: Michel
authors.initials: M
authors.lastname: Jaquinod
authors.forename: Mathieu
authors.initials: M
authors.lastname: Trauchessec
authors.forename: Céline
authors.initials: C
authors.lastname: Huillet
authors.forename: Mathilde
authors.initials: M
authors.lastname: Louwagie
authors.forename: Dorothée
authors.initials: D
authors.lastname: Lebert
authors.forename: Guillaume
authors.initials: G
authors.lastname: Picard
authors.forename: Annie
authors.initials: A
authors.lastname: Adrait
authors.forename: Alain
authors.initials: A
authors.lastname: Dupuis
authors.forename: Jérôme
authors.initials: J
authors.lastname: Garin
authors.forename: Virginie
authors.initials: V
authors.lastname: Brun
authors.forename: Christophe
authors.initials: C
authors.lastname: Bruley
mesh_terms: D020816:Amino Acid Motifs; D001120:Arginine / Q000737:chemistry; D002853:Chromatography, Liquid / Q000379:methods*; D003545:Cysteine / Q000737:chemistry; D006801:Humans; D007553:Isotope Labeling; D008239:Lysine / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008715:Methionine / Q000737:chemistry; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000097:blood; D059748:Proteolysis; D040901:Proteomics / Q000379:methods*; D011865:Radioisotope Dilution Technique; D012015:Reference Standards; D014357:Trypsin / Q000737:chemistry
chemical_list: D010455:Peptides; D001120:Arginine; D008715:Methionine; D014357:Trypsin; D008239:Lysine; D003545:Cysteine