title: Improving qualitative and quantitative performance for MS(E)-based label-free proteomics.
abstract: Label-free quantitation by data independent methods (for instance MS(E)) is growing in popularity due to the high technical reproducibility of mass spectrometry analysis. The recent introduction of Synapt hybrid instruments capable of incorporating ion mobility separation within mass spectrometry analysis now allows acquisition of high definition MS(E) data (HDMS(E)). HDMS(E) enables deeper proteome coverage and more confident peptide identifications when compared to MS(E), while the latter offers a higher dynamic range for quantitation. We have developed synapter as, a versatile tool to better evaluate the results of data independent acquisitions on Waters instruments. We demonstrate that synapter can be used to combine HDMS(E) and MS(E) data to achieve deeper proteome coverage delivered by HDMS(E) and more accurate quantitation for high intensity peptides, delivered by MS(E). For users who prefer to run samples exclusively in one mode, synapter allows other useful functionality like false discovery rate estimation, filtering on peptide match type and mass error, and filling missing values. Our software integrates with existing tools, thus permitting us to easily combine peptide quantitation information into protein quantitation by a range of different approaches.
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Bond
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Shliaha
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
authors.forename: Laurent
authors.initials: L
authors.lastname: Gatto
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000032:analysis* / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods / Q000706:statistics & numerical data*; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D010455:Peptides