When less can yield more – Computational preprocessing of MS/MS spectra for peptide identification |
| |
| Authors: | Bernhard Y. Renard Marc Kirchner Flavio Monigatti Alexander R. Ivanov Juri Rappsilber Dominic Winter Judith A. J. Steen Fred A. Hamprecht Hanno Steen |
| |
| Affiliation: | 1. Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany;2. Proteomics Center, Children's Hospital, Boston, MA, USA;3. Department of Pathology, Harvard Medical School and Children's Hospital, Boston, MA, USA;4. Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA;5. Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK;6. Department of Neurobiology, Harvard Medical School and Department of Neurology, Children's Hospital, Boston, MA, USA |
| |
| Abstract: | The effectiveness of database search algorithms, such as Mascot, Sequest and ProteinPilot is limited by the quality of the input spectra: spurious peaks in MS/MS spectra can jeopardize the correct identification of peptides or reduce their score significantly. Consequently, an efficient preprocessing of MS/MS spectra can increase the sensitivity of peptide identification at reduced file sizes and run time without compromising its specificity. We investigate the performance of 25 MS/MS preprocessing methods on various data sets and make software for improved preprocessing of mgf/dta‐files freely available from http://hci.iwr.uni‐heidelberg.de/mip/proteomics or http://www.childrenshospital.org/research/steenlab . |
| |
| Keywords: | |
|
|
