Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean
Top Cited Papers
- 2 July 2009
- journal article
- research article
- Published by American Chemical Society (ACS) in Analytical Chemistry
- Vol. 81 (15) , 6481-6488
- https://doi.org/10.1021/ac900888s
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. Here, we demonstrate the superior performance of a data-independent method we term precursor acquisition independent from ion count (PAcIFIC). Our results show that almost the entire, predicted, soluble bacterial proteome can be thoroughly analyzed by PAcIFIC without the need for any sample fractionation other than the C18-based liquid chromatograph used to introduce the peptide mixture into the mass spectrometer. Importantly, we also show that PAcIFIC provides unique performance for analysis of human plasma in terms of the number of proteins identified (746 at FDR ≤ 0.5%) and achieved dynamic range (8 orders of magnitude at FDR ≤ 0.5%), without any fractionation other than immuno-depletion of the seven most abundant proteins.Keywords
This publication has 29 references indexed in Scilit:
- Increasing information from shotgun proteomic data by accounting for misassigned precursor ion massesProteomics, 2008
- A mouse plasma peptide atlas as a resource for disease proteomicsGenome Biology, 2008
- On the benefits of acquiring peptide fragment ions at high measured mass accuracyJournal of the American Society for Mass Spectrometry, 2008
- A Qit‐q‐Tof mass spectrometer for two‐dimensional tandem mass spectrometryRapid Communications in Mass Spectrometry, 2007
- High-Speed Data Reduction, Feature Detection, and MS/MS Spectrum Quality Assessment of Shotgun Proteomics Data Sets Using High-Resolution Mass SpectrometryAnalytical Chemistry, 2007
- Structural heterogeneity and environmentally regulated remodeling of Francisella tularensis subspecies novicida lipid a characterized by tandem mass spectrometryJournal of the American Society for Mass Spectrometry, 2007
- Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectraNature Methods, 2004
- Shotgun collision‐induced dissociation of peptides using a time of flight mass analyzerProteomics, 2003
- Mass spectrometry-based proteomicsNature, 2003
- An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseJournal of the American Society for Mass Spectrometry, 1994