title: Faster, quantitative, and accurate precursor acquisition independent from ion count.
abstract: Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Recently, we demonstrated the superior performance of a data-independent method we termed precursor acquisition independent from ion count (PAcIFIC). Here, we report a faster, accurate, multiplexed, and quantitative PAcIFIC method. Our results show that the time needed to perform such analysis can be decreased by 33% to 66% using modern ion trap instruments and that high mass accuracy can be applied to such a strategy. Quantification capability is demonstrated on protein standards and a whole bacterial cell lysate using isobaric tagging. Finally, we confirm in yeast the dynamic range capabilities of such a method where proteins down to less than 50 copies per cell can be monitored without sample prefractionation.
authors.affiliation: Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Panchaud
authors.forename: Sunhee
authors.initials: S
authors.lastname: Jung
authors.forename: Scott A
authors.initials: SA
authors.lastname: Shaffer
authors.forename: John D
authors.initials: JD
authors.lastname: Aitchison
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
mesh_terms: D000818:Animals; D002417:Cattle; D030562:Databases, Protein; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry; D013997:Time Factors
chemical_list: D010455:Peptides