title: The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides.
abstract: Mass spectrometric characterization of protein modifications is usually based on single peptides. With the advent of large-scale PTM-focussed MS studies, vast amounts of data are generated continuously, providing biologists extremely valuable and virtually never-ending sources for targeted functional research. However, even more than for proteomics in general, appropriate strategies for quality control of the different steps of the analytical strategy are imperative to prevent functional researchers from doing Sisyphos work on false-positive and unconfident PTM assignments. Here, we describe strategies to address the important issue of quality control for PTM analysis on various levels of the analytical pipeline: sample preparation/processing, analysis/identification and finally data interpretation, for qualitative as well as quantitative studies.
authors.affiliation: Leibniz Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Beck
authors.forename: Urs
authors.initials: U
authors.lastname: Lewandrowski
authors.forename: Matthias
authors.initials: M
authors.lastname: Wiltfang
authors.forename: Ingo
authors.initials: I
authors.lastname: Feldmann
authors.forename: Jörg
authors.initials: J
authors.lastname: Geiger
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
authors.forename: René Peiman
authors.initials: RP
authors.lastname: Zahedi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid; D003627:Data Interpretation, Statistical; D030562:Databases, Protein / Q000706:statistics & numerical data; D006031:Glycosylation; D006801:Humans; D010455:Peptides / Q000737:chemistry* / Q000302:isolation & purification; D040901:Proteomics / Q000592:standards* / Q000706:statistics & numerical data; D011786:Quality Control; D057386:Search Engine; D012984:Software; D053719:Tandem Mass Spectrometry / Q000592:standards* / Q000706:statistics & numerical data; D014025:Titanium
chemical_list: D010455:Peptides; C009495:titanium dioxide; D014025:Titanium