Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting
Publication type: Journal Article
Publication date: 2018-12-27
scimago Q2
wos Q1
SJR: 0.983
CiteScore: 5.7
Impact factor: 3.9
ISSN: 16159853, 16159861
PubMed ID:
30537264
Biochemistry
Molecular Biology
Abstract
Shotgun proteomics workflows for database protein identification typically include a combination of search engines and postsearch validation software based mostly on machine learning algorithms. Here, a new postsearch validation tool called Scavager employing CatBoost, an open-source gradient boosting library, which shows improved efficiency compared with the other popular algorithms, such as Percolator, PeptideProphet, and Q-ranker, is presented. The comparison is done using multiple data sets and search engines, including MSGF+, MSFragger, X!Tandem, Comet, and recently introduced IdentiPy. Implemented in Python programming language, Scavager is open-source and freely available at https://bitbucket.org/markmipt/scavager.
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Metrics
58
Total citations:
58
Citations from 2024:
10
(17%)
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GOST
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Ivanov M. et al. Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting // Proteomics. 2018. Vol. 19. No. 3. p. 1800280.
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Ivanov M., Levitsky L., Bubis J. A., Gorshkov M. V. Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting // Proteomics. 2018. Vol. 19. No. 3. p. 1800280.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1002/pmic.201800280
UR - https://doi.org/10.1002/pmic.201800280
TI - Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting
T2 - Proteomics
AU - Ivanov, Mark
AU - Levitsky, Lev
AU - Bubis, Julia A
AU - Gorshkov, Mikhail V.
PY - 2018
DA - 2018/12/27
PB - Wiley
SP - 1800280
IS - 3
VL - 19
PMID - 30537264
SN - 1615-9853
SN - 1615-9861
ER -
Cite this
BibTex (up to 50 authors)
Copy
@article{2018_Ivanov,
author = {Mark Ivanov and Lev Levitsky and Julia A Bubis and Mikhail V. Gorshkov},
title = {Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting},
journal = {Proteomics},
year = {2018},
volume = {19},
publisher = {Wiley},
month = {dec},
url = {https://doi.org/10.1002/pmic.201800280},
number = {3},
pages = {1800280},
doi = {10.1002/pmic.201800280}
}
Cite this
MLA
Copy
Ivanov, Mark, et al. “Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting.” Proteomics, vol. 19, no. 3, Dec. 2018, p. 1800280. https://doi.org/10.1002/pmic.201800280.
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