title: Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation.
abstract: Application of iTRAQ-based workflows for protein profiling has become widespread. Concomitantly, the idiosyncratic limitations of iTRAQ, such as its tendency to underestimate quantifications, have been studied and recognised. This report shows that the influence of ratio compression and limiting transmission in iTRAQ MS/MS in high-complexity mixtures (iTRAQ-labelled lysates) can be partly alleviated using high-resolution sample fractionation. Here, we also investigate in greater detail the dependency of iTRAQ quantification on the dynamics of online chromatography in low-complexity mixtures (iTRAQ-labelled standards). These findings will allow more efficient strategies to be designed for iTRAQ proteomics, alleviating iTRAQ underestimation and thus facilitating the detection of subtle abundance changes.
authors.affiliation: ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.
authors.forename: Saw Yen
authors.initials: SY
authors.lastname: Ow
authors.forename: Malinda
authors.initials: M
authors.lastname: Salim
authors.forename: Josselin
authors.initials: J
authors.lastname: Noirel
authors.forename: Caroline
authors.initials: C
authors.lastname: Evans
authors.forename: Phillip C
authors.initials: PC
authors.lastname: Wright
mesh_terms: D002852:Chromatography, Ion Exchange / Q000379:methods*; D057927:Hydrophobic and Hydrophilic Interactions; D007553:Isotope Labeling / Q000379:methods*; D016014:Linear Models; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins