title: Hybrid data acquisition and processing strategies with increased throughput and selectivity: pSMART analysis for global qualitative and quantitative analysis.
abstract: Data-dependent acquisition (DDA) and data-independent acquisition strategies (DIA) have both resulted in improved understanding of proteomics samples. Both strategies have advantages and disadvantages that are well-published, where DDA is typically applied for deep discovery and DIA may be used to create sample records. In this paper, we present a hybrid data acquisition and processing strategy (pSMART) that combines the strengths of both techniques and provides significant benefits for qualitative and quantitative peptide analysis. The performance of pSMART is compared to published DIA strategies in an experiment that allows the objective assessment of DIA performance with respect to interrogation of previously acquired MS data. The results of this experiment demonstrate that pSMART creates fewer decoy hits than a standard DIA strategy. Moreover, we show that pSMART is more selective, sensitive, and reproducible than either standard DIA or DDA strategies alone.
authors.affiliation: Thermo Fisher Scientific, 790 Memorial Drive, Suite 202, Cambridge, Massachusetts 02139, United States.
authors.forename: Amol
authors.initials: A
authors.lastname: Prakash
authors.forename: Scott
authors.initials: S
authors.lastname: Peterman
authors.forename: Shadab
authors.initials: S
authors.lastname: Ahmad
authors.forename: David
authors.initials: D
authors.lastname: Sarracino
authors.forename: Barbara
authors.initials: B
authors.lastname: Frewen
authors.forename: Maryann
authors.initials: M
authors.lastname: Vogelsang
authors.forename: Gregory
authors.initials: G
authors.lastname: Byram
authors.forename: Bryan
authors.initials: B
authors.lastname: Krastins
authors.forename: Gouri
authors.initials: G
authors.lastname: Vadali
authors.forename: Mary
authors.initials: M
authors.lastname: Lopez
mesh_terms: D000595:Amino Acid Sequence; D002853:Chromatography, Liquid / Q000379:methods; D001330:Electronic Data Processing / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000378:metabolism; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D010455:Peptides; D020543:Proteome
keywords: Fourier transform; data-independent analysis; decoy searching; mass spectrometry; peptide; qualitative; quantitative