التفاصيل البيبلوغرافية
| العنوان: |
A flexible statistical model for alignment of label-free proteomics data - incorporating ion mobility and product ion information. |
| المؤلفون: |
Benjamin, Ashlee M., Thompson, J. Will., Soderblom, Erik J., Geromanos, Scott J., Henao, Ricardo, Kraus, Virginia B., Moseley, M. Arthur, Lucas, Joseph E. |
| المصدر: |
BMC Bioinformatics; 2013, Vol. 14 Issue 1, p1-25, 25p, 1 Diagram, 1 Chart, 4 Graphs |
| مصطلحات موضوعية: |
PROTEOMICS, ION mobility, PEPTIDES, STATISTICAL matching, DAUGHTER ions |
| مستخلص: |
Background The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these informationrich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing - the matching of peptide measurements across samples. Results We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Conclusions Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods. [ABSTRACT FROM AUTHOR] |
|
Copyright of BMC Bioinformatics is the property of BioMed Central and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) |
| قاعدة البيانات: |
Complementary Index |
Full Text Finder