PROTEIN IDENTIFICATION USING SEQUENCE DATABASES

The bottom-up proteomics approach (also known as the shotgun approach), based on the digestion of proteins in peptides and their sequencing using tandem mass spectrometry (MS/MS), has become widespread. The identification of peptides from the obtained MS/MS data is most often done using available se...

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Autores principales:	Golenko Ye., A. Ismailova, Ye. Rais
Formato:	article
Lenguaje:	EN
Publicado:	Astana IT University 2020
Materias:	mass spectrometry, ms/ms, bioinformatics, protein identification, proteomics, databases, protein sequence Information technology T58.5-58.64
Acceso en línea:	https://doaj.org/article/08fbef719d8b473fab7c4074159c58b0
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spelling	oai:doaj.org-article:08fbef719d8b473fab7c4074159c58b02021-12-02T13:00:20ZPROTEIN IDENTIFICATION USING SEQUENCE DATABASES2707-90312707-904Xhttps://doaj.org/article/08fbef719d8b473fab7c4074159c58b02020-09-01T00:00:00Zhttp://ojs.astanait.edu.kz/index.php/sjaitu/article/view/33https://doaj.org/toc/2707-9031https://doaj.org/toc/2707-904XThe bottom-up proteomics approach (also known as the shotgun approach), based on the digestion of proteins in peptides and their sequencing using tandem mass spectrometry (MS/MS), has become widespread. The identification of peptides from the obtained MS/MS data is most often done using available sequence databases. This paper presents a detailed overview of the peptide identification workflow and a description of the main protein bioinformatics databases. Choosing the correct search parameters and the sequence database is essential to the success of this method, and we pay special attention to the practical aspects of searching for efficient analysis of MS/MS spectra. We also consider possible reasons why database search tools cannot find the correct sequence for some MS/MS spectra and highlight the misidentification issues that can significantly reduce the value of published data. To help assess the assignment of peptides to MS/MS spectra, we will look at the scoring algorithms that are used in the most popular database search tools. We also analyze statistical methods and computational tools for validating peptide compliance with MS/MS data. The final part describes the process of determining the identity of protein samples from a list of peptide identifications and discusses the limitations of bottom-up proteomics.Golenko Ye.A. IsmailovaYe. RaisAstana IT Universityarticlemass spectrometry, ms/ms, bioinformatics, protein identification, proteomics, databases, protein sequenceInformation technologyT58.5-58.64ENScientific Journal of Astana IT University, Vol 0, Iss 4, Pp 14-23 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	mass spectrometry, ms/ms, bioinformatics, protein identification, proteomics, databases, protein sequence Information technology T58.5-58.64
spellingShingle	mass spectrometry, ms/ms, bioinformatics, protein identification, proteomics, databases, protein sequence Information technology T58.5-58.64 Golenko Ye. A. Ismailova Ye. Rais PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
description	The bottom-up proteomics approach (also known as the shotgun approach), based on the digestion of proteins in peptides and their sequencing using tandem mass spectrometry (MS/MS), has become widespread. The identification of peptides from the obtained MS/MS data is most often done using available sequence databases. This paper presents a detailed overview of the peptide identification workflow and a description of the main protein bioinformatics databases. Choosing the correct search parameters and the sequence database is essential to the success of this method, and we pay special attention to the practical aspects of searching for efficient analysis of MS/MS spectra. We also consider possible reasons why database search tools cannot find the correct sequence for some MS/MS spectra and highlight the misidentification issues that can significantly reduce the value of published data. To help assess the assignment of peptides to MS/MS spectra, we will look at the scoring algorithms that are used in the most popular database search tools. We also analyze statistical methods and computational tools for validating peptide compliance with MS/MS data. The final part describes the process of determining the identity of protein samples from a list of peptide identifications and discusses the limitations of bottom-up proteomics.
format	article
author	Golenko Ye. A. Ismailova Ye. Rais
author_facet	Golenko Ye. A. Ismailova Ye. Rais
author_sort	Golenko Ye.
title	PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
title_short	PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
title_full	PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
title_fullStr	PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
title_full_unstemmed	PROTEIN IDENTIFICATION USING SEQUENCE DATABASES
title_sort	protein identification using sequence databases
publisher	Astana IT University
publishDate	2020
url	https://doaj.org/article/08fbef719d8b473fab7c4074159c58b0
work_keys_str_mv	AT golenkoye proteinidentificationusingsequencedatabases AT aismailova proteinidentificationusingsequencedatabases AT yerais proteinidentificationusingsequencedatabases
_version_	1718393547592302592

PROTEIN IDENTIFICATION USING SEQUENCE DATABASES

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