title: The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition.
abstract: As tryptic peptides and metabolites are not equally distributed along the mass range, the probability of cross fragment ion interference is higher in certain windows when fixed Q1 SWATH windows are applied. We evaluated the benefits of utilizing variable Q1 SWATH windows with regards to selectivity improvement. Variable windows based on equalizing the distribution of either the precursor ion population (PIP) or the total ion current (TIC) within each window were generated by an in-house software, swathTUNER. These two variable Q1 SWATH window strategies outperformed, with respect to quantification and identification, the basic approach using a fixed window width (FIX) for proteomic profiling of human monocyte-derived dendritic cells (MDDCs). Thus, 13.8 and 8.4% additional peptide precursors, which resulted in 13.1 and 10.0% more proteins, were confidently identified by SWATH using the strategy PIP and TIC, respectively, in the MDDC proteomic sample. On the basis of the spectral library purity score, some improvement warranted by variable Q1 windows was also observed, albeit to a lesser extent, in the metabolomic profiling of human urine. We show that the novel concept of "scheduled SWATH" proposed here, which incorporates (i) variable isolation windows and (ii) precursor retention time segmentation further improves both peptide and metabolite identifications.
authors: University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland.
authors: Ying
authors: Y
authors: Zhang
authors: University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland.|SIB Swiss Institute of Bioinformatics , Proteome Informatics Group, Geneva, Switzerland.
authors: Aivett
authors: A
authors: Bilbao
authors: University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland.
authors: Tobias
authors: T
authors: Bruderer
authors: University of Massachusetts , Medical School, Program in Molecular Medicine, Worcester, Massachusetts 01605, United States.
authors: Jeremy
authors: J
authors: Luban
authors: University of Massachusetts , Medical School, Program in Molecular Medicine, Worcester, Massachusetts 01605, United States.
authors: Caterina
authors: C
authors: Strambio-De-Castillia
authors: SIB Swiss Institute of Bioinformatics , Proteome Informatics Group, Geneva, Switzerland.|University of Geneva , Faculty of Sciences, Geneva, Switzerland.
authors: Frédérique
authors: F
authors: Lisacek
authors: University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland.
authors: Gérard
authors: G
authors: Hopfgartner
authors: University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland.
authors: Emmanuel
authors: E
authors: Varesio
mesh_terms: D000595:Amino Acid Sequence; D056148:Chromatography, Reverse-Phase; D003713:Dendritic Cells / Q000737:chemistry*; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000652:urine*; D061251:Primary Cell Culture; D059748:Proteolysis; D020543:Proteome / Q000302:isolation & purification*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D014357:Trypsin / Q000737:chemistry
chemical_list: D010455:Peptides; D020543:Proteome; D014357:Trypsin
keywords: SWATH; metabolomics; proteomics; selectivity; variable Q1 window widths