IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics
Lev Levitsky
1, 2
,
Mark Ivanov
2
,
Anna A. Lobas
2
,
Julia A Bubis
2
,
Irina A Tarasova
2
,
Elizaveta M. Solovyeva
2
,
Publication type: Journal Article
Publication date: 2018-04-23
scimago Q1
wos Q2
SJR: 1.139
CiteScore: 7.3
Impact factor: 3.6
ISSN: 15353893, 15353907
PubMed ID:
29682971
General Chemistry
Biochemistry
Abstract
We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel "autotune" feature, IdentiPy outperforms the popular alternatives on high-resolution data sets. Autotune adjusts the search parameters for the particular data set, resulting in improved search efficiency and simplifying the user experience. IdentiPy with the autotune feature shows higher sensitivity compared with the evaluated search engines. IdentiPy Server has built-in postprocessing and protein inference procedures and provides graphic visualization of the statistical properties of the data set and the search results. It is open-source and can be freely extended to use third-party scoring functions or processing algorithms and allows customization of the search workflow for specialized applications.
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61
Total citations:
61
Citations from 2024:
10
(16%)
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MLA
Cite this
GOST
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Levitsky L. et al. IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics // Journal of Proteome Research. 2018. Vol. 17. No. 7. pp. 2249-2255.
GOST all authors (up to 50)
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Levitsky L., Ivanov M., Lobas A. A., Bubis J. A., Tarasova I. A., Solovyeva E. M., Pridatchenko M. L., Gorshkov M. V. IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics // Journal of Proteome Research. 2018. Vol. 17. No. 7. pp. 2249-2255.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1021/acs.jproteome.7b00640
UR - https://doi.org/10.1021/acs.jproteome.7b00640
TI - IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics
T2 - Journal of Proteome Research
AU - Levitsky, Lev
AU - Ivanov, Mark
AU - Lobas, Anna A.
AU - Bubis, Julia A
AU - Tarasova, Irina A
AU - Solovyeva, Elizaveta M.
AU - Pridatchenko, Marina L
AU - Gorshkov, Mikhail V.
PY - 2018
DA - 2018/04/23
PB - American Chemical Society (ACS)
SP - 2249-2255
IS - 7
VL - 17
PMID - 29682971
SN - 1535-3893
SN - 1535-3907
ER -
Cite this
BibTex (up to 50 authors)
Copy
@article{2018_Levitsky,
author = {Lev Levitsky and Mark Ivanov and Anna A. Lobas and Julia A Bubis and Irina A Tarasova and Elizaveta M. Solovyeva and Marina L Pridatchenko and Mikhail V. Gorshkov},
title = {IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics},
journal = {Journal of Proteome Research},
year = {2018},
volume = {17},
publisher = {American Chemical Society (ACS)},
month = {apr},
url = {https://doi.org/10.1021/acs.jproteome.7b00640},
number = {7},
pages = {2249--2255},
doi = {10.1021/acs.jproteome.7b00640}
}
Cite this
MLA
Copy
Levitsky, Lev, et al. “IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics.” Journal of Proteome Research, vol. 17, no. 7, Apr. 2018, pp. 2249-2255. https://doi.org/10.1021/acs.jproteome.7b00640.