Identification of proteins from proteomic analysis

Zainab Noor; Abidali Mohamedali; Shoba Ranganathan

doi:10.1016/B978-0-323-95502-7.00363-8

Identification of proteins from proteomic analysis

Zainab Noor, Abidali Mohamedali, Shoba Ranganathan

Research output: Chapter in Book/Report/Conference proceeding › Entry for encyclopedia/dictionary/reference book › peer-review

Abstract

Mass spectrometry based identification of proteins is one of the foundations of proteomics. In recent decades, this post-genomic discipline has been widely used in all fields in biology from biomarker discovery in human diseases to markers of freshness in fruit. In this chapter, we present the basic mechanism of data acquisition through a mass spectrometer, and extraction and analysis of protein identities using readily available, web based bioinformatics and computational tools. A sample yeast dataset is used to illustrate the process of protein identification based on the Trans-Proteomic pipeline, as well as other web tools. To increase the confidence in protein identity, communally accepted metrics are also suggested.

Original language	English
Title of host publication	Encyclopedia of Bioinformatics and Computational Biology
Editors	Shoba Ranganathan, Mario Cannataro, Asif M. Khan
Place of Publication	Oxford
Publisher	Elsevier
Pages	454-469
Number of pages	16
Volume	5
Edition	2nd
ISBN (Electronic)	9780323955027
ISBN (Print)	9780323955034
DOIs	https://doi.org/10.1016/B978-0-323-95502-7.00363-8
Publication status	Published - 2025

Keywords

Bioinformatics
Data processing
Databases
Protein annotation
Protein identification
Proteomics data analysis
Shotgun proteomics
Tandem mass spectrometry
Trans-Proteomic pipeline
Web resources

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10.1016/B978-0-323-95502-7.00363-8

Cite this

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title = "Identification of proteins from proteomic analysis",

abstract = "Mass spectrometry based identification of proteins is one of the foundations of proteomics. In recent decades, this post-genomic discipline has been widely used in all fields in biology from biomarker discovery in human diseases to markers of freshness in fruit. In this chapter, we present the basic mechanism of data acquisition through a mass spectrometer, and extraction and analysis of protein identities using readily available, web based bioinformatics and computational tools. A sample yeast dataset is used to illustrate the process of protein identification based on the Trans-Proteomic pipeline, as well as other web tools. To increase the confidence in protein identity, communally accepted metrics are also suggested.",

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Identification of proteins from proteomic analysis. / Noor, Zainab; Mohamedali, Abidali ; Ranganathan, Shoba.
Encyclopedia of Bioinformatics and Computational Biology. ed. / Shoba Ranganathan; Mario Cannataro; Asif M. Khan. Vol. 5 2nd. ed. Oxford: Elsevier, 2025. p. 454-469.

Research output: Chapter in Book/Report/Conference proceeding › Entry for encyclopedia/dictionary/reference book › peer-review

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KW - Data processing

KW - Databases

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KW - Protein identification

KW - Proteomics data analysis

KW - Shotgun proteomics

KW - Tandem mass spectrometry

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BT - Encyclopedia of Bioinformatics and Computational Biology

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PB - Elsevier

CY - Oxford

ER -

Identification of proteins from proteomic analysis

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Keywords

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