TY - JOUR
T1 - When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification
AU - Renard, Bernard Y.
AU - Kirchner, Marc
AU - Monigatti, Flavio
AU - Ivanov, Alexander R.
AU - Rappsilber, Juri
AU - Winter, Dominic
AU - Steen, Judith A.J.
AU - Hamprecht, Fred A.
AU - Steen, Hanno
PY - 2009/11/30
Y1 - 2009/11/30
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?partnerID=yv4JPVwI&eid=2-s2.0-70350449457&md5=4c41b9776595032f095a2cd914d8a693
U2 - 10.1002/pmic.200900326
DO - 10.1002/pmic.200900326
M3 - Article
C2 - 19743429
AN - SCOPUS:70350449457
VL - 9
SP - 4978
EP - 4984
JO - Proteomics
JF - Proteomics
SN - 1615-9853
IS - 21
ER -