These authors contributed equally to this work.
Precursor ion exclusion for enhanced identification of plasma biomarkers
Article first published online: 29 JUN 2012
© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
PROTEOMICS - Clinical Applications
Volume 6, Issue 5-6, pages 304–308, June 2012
How to Cite
Wu, W. W., Shen, R.-F., Park, S.-S., Martin, B. and Maudsley, S. (2012), Precursor ion exclusion for enhanced identification of plasma biomarkers. Prot. Clin. Appl., 6: 304–308. doi: 10.1002/prca.201100107
Colour Online: See the article online to view Fig. 3 in colour.
- Issue published online: 29 JUN 2012
- Article first published online: 29 JUN 2012
- Accepted manuscript online: 29 MAY 2012 02:04AM EST
- Manuscript Accepted: 6 MAR 2012
- Manuscript Revised: 6 FEB 2012
- Manuscript Received: 13 DEC 2011
- Intramural Research Programs of National Institute on Aging
- National Institutes of Health
- Multi-dimensional fractionation;
- Plasma biomarkers;
- Precursor ion exclusion
Our study aims to establish a plasma biomarker analysis workflow, with fewer fractionation steps, for enhanced identification of plasma biomarkers by precursor ion exclusion (PIE).
Plasma samples were depleted for highly abundant proteins, then further fractionated by molecular weight (MW), before trypsinization for LTQ-Orbitrap mass analysis. Data-dependent acquisition (DDA) was used for baseline analysis. PIE involves the re-injection of samples with exclusion of the previously identified peptides. We compared analyses using multiple PIE iterations, compared to DDA, for plasma interrogation
A higher percentage of unique plasma peptides was identified with PIE, compared to DDA. The first PIE iteration reveals an increase of 75–112% more peptides than the DDA method alone. PIE can interrogate complex plasma samples with the percentage of peptides identified successively increasing with even ≥4 iterations. The total number of peptides identified increases rapidly across the first three PIE iterations and then continues more slowly up to nine iterations.
Conclusions and clinical relevance
Iterative injections with PIE resulted in many more peptide identifications in plasma samples of varying degrees of complexity, compared to re-injections using similar DDA parameters. PIE methods may therefore expand our ability to recover plasma peptides for plasma biomarker discovery.