TY - JOUR
T1 - Crescendo
T2 - A protein sequence database search engine for tandem mass spectra
AU - Wang, Jianqi
AU - Zhang, Yajie
AU - Yu, Yonghao
N1 - Publisher Copyright:
© 2015 American Society for Mass Spectrometry.
PY - 2015/7/22
Y1 - 2015/7/22
N2 - A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L-and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm. [Figure not available: see fulltext.]
AB - A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L-and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm. [Figure not available: see fulltext.]
KW - Peptide-spectrum match
KW - Search engine
KW - Tandem mass spectrometry
UR - http://www.scopus.com/inward/record.url?scp=84935026220&partnerID=8YFLogxK
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U2 - 10.1007/s13361-015-1120-3
DO - 10.1007/s13361-015-1120-3
M3 - Article
C2 - 25895889
AN - SCOPUS:84935026220
SN - 1044-0305
VL - 26
SP - 1077
EP - 1084
JO - Journal of the American Society for Mass Spectrometry
JF - Journal of the American Society for Mass Spectrometry
IS - 7
ER -