Faster, quantitative, and accurate precursor acquisition independent from ion count

TitleFaster, quantitative, and accurate precursor acquisition independent from ion count
Publication TypeJournal Article
Year of Publication2011
AuthorsPanchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR
JournalAnal Chem
Volume83
Pagination2250-7
Date PublishedMar 15
PMID21341720
AbstractData-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.

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