title: Quantitation of the phosphoproteome using the library-assisted extracted ion chromatogram (LAXIC) strategy.
abstract: Phosphorylation is a key posttranslational modification that regulates many signaling pathways, but quantifying changes in phosphorylation between samples can be challenging due to its low stoichiometry within cells. We have introduced a mass spectrometry-based label-free quantitation strategy termed LAXIC for the analysis of the phosphoproteome. This method uses a spiked-in synthetic peptide library designed to elute across the entire chromatogram for local normalization of phosphopeptides within complex samples. Normalization of phosphopeptides by library peptides that co-elute within a small time frame accounts for fluctuating ion suppression effects, allowing more accurate quantitation even when LC-MS performance varies. Here we explain the premise of LAXIC, the design of a suitable peptide library, and how the LAXIC algorithm can be implemented with software developed in-house.
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN, USA.
authors.forename: Justine V
authors.initials: JV
authors.lastname: Arrington
authors.forename: Liang
authors.initials: L
authors.lastname: Xue
authors.forename: W Andy
authors.initials: WA
authors.lastname: Tao
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry; D010750:Phosphoproteins / Q000737:chemistry*; D020543:Proteome
chemical_list: D010750:Phosphoproteins; D020543:Proteome