tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

Hyoung Sam Heo; Sanghyuk Lee; Ji Min Kim; Yeon Ja Choi; Hae Young Chung; S. June Oh

doi:10.1016/j.bbrc.2010.05.093

tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

Hyoung Sam Heo, Sanghyuk Lee, Ji Min Kim, Yeon Ja Choi, Hae Young Chung, S. June Oh

Department of Life Science

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

Peptide mass fingerprinting (PMF) has become one of the most widely used methods for rapid identification of proteins in proteomics research. Many peaks, however, remain unassigned after PMF analysis, partly because of post-translational modification and the limited scope of protein sequences. Almost all PMF tools employ only known or predicted protein sequences and do not include open reading frames (ORFs) in the genome, which eliminates the chance of finding novel functional peptides. Unlike most tools that search protein sequences from known coding sequences, the tool we developed uses a database for theoretical small ORFs (tsORFs) and a PMF application using a tsORFs database (tsORFdb). The tsORFdb is a database for ORFeome that encompasses all potential tsORFs derived from whole genome sequences as well as the predicted ones. The massProphet system tries to extend the search scope to include the ORFeome using the tsORFdb. The tsORFdb and massProphet should be useful for proteomics research to give information about unknown small ORFs as well as predicted and registered proteins.

Original language	English
Pages (from-to)	120-126
Number of pages	7
Journal	Biochemical and Biophysical Research Communications
Volume	397
Issue number	1
DOIs	https://doi.org/10.1016/j.bbrc.2010.05.093
State	Published - 18 Jun 2010

Bibliographical note

Funding Information:
This work was supported by and a National Research Foundation of Korea (NRF) grant (No. 2009-0083538) funded by the Korea government (MEST) and the 2005 Inje University research grant. We are grateful to the ‘Aging Tissue Bank’ for supplying research resources.

Keywords

Bioinformatics
Database
ORFeomics
Peptide Mass Fingerprinting
Proteomics
sORFs (Small Open Reading Frames)

Access to Document

10.1016/j.bbrc.2010.05.093

Cite this

@article{c856a49ac45549228da4b81255591861,

title = "tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs",

abstract = "Peptide mass fingerprinting (PMF) has become one of the most widely used methods for rapid identification of proteins in proteomics research. Many peaks, however, remain unassigned after PMF analysis, partly because of post-translational modification and the limited scope of protein sequences. Almost all PMF tools employ only known or predicted protein sequences and do not include open reading frames (ORFs) in the genome, which eliminates the chance of finding novel functional peptides. Unlike most tools that search protein sequences from known coding sequences, the tool we developed uses a database for theoretical small ORFs (tsORFs) and a PMF application using a tsORFs database (tsORFdb). The tsORFdb is a database for ORFeome that encompasses all potential tsORFs derived from whole genome sequences as well as the predicted ones. The massProphet system tries to extend the search scope to include the ORFeome using the tsORFdb. The tsORFdb and massProphet should be useful for proteomics research to give information about unknown small ORFs as well as predicted and registered proteins.",

keywords = "Bioinformatics, Database, ORFeomics, Peptide Mass Fingerprinting, Proteomics, sORFs (Small Open Reading Frames)",

author = "Heo, {Hyoung Sam} and Sanghyuk Lee and Kim, {Ji Min} and Choi, {Yeon Ja} and Chung, {Hae Young} and {June Oh}, S.",

note = "Funding Information: This work was supported by and a National Research Foundation of Korea (NRF) grant (No. 2009-0083538) funded by the Korea government (MEST) and the 2005 Inje University research grant. We are grateful to the {\textquoteleft}Aging Tissue Bank{\textquoteright} for supplying research resources. ",

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doi = "10.1016/j.bbrc.2010.05.093",

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tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs. / Heo, Hyoung Sam; Lee, Sanghyuk; Kim, Ji Min et al.
In: Biochemical and Biophysical Research Communications, Vol. 397, No. 1, 18.06.2010, p. 120-126.

Research output: Contribution to journal › Article › peer-review

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