Identification of proteins from proteomic analysis

Zainab Noor; Abidali Mohamedali; Shoba Ranganathan

doi:10.1016/B978-0-12-809633-8.20478-0

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

1 Citation (Scopus)

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
Subtitle of host publication	ABC of Bioinformatics
Editors	Mario Cannataro, Bruno Gaeta, Mohammad Asif Khan
Place of Publication	Amsterdam; Oxford; Cambridge
Publisher	Elsevier
Pages	855-870
Number of pages	16
Volume	3
ISBN (Electronic)	9780128114322
ISBN (Print)	9780128114148
DOIs	https://doi.org/10.1016/B978-0-12-809633-8.20478-0
Publication status	Published - 2019

Bibliographical note

Editors-in-chief: Shoba Ranganathan, Kenta Nakai, Christian Schönbach, Michael Gribskov.

Keywords

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

Access to Document

10.1016/B978-0-12-809633-8.20478-0

Cite this

@inbook{78634de483e442159ece2338ed561521,

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.",

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

author = "Zainab Noor and Abidali Mohamedali and Shoba Ranganathan",

note = "Editors-in-chief: Shoba Ranganathan, Kenta Nakai, Christian Sch{\"o}nbach, Michael Gribskov.",

year = "2019",

doi = "10.1016/B978-0-12-809633-8.20478-0",

language = "English",

isbn = "9780128114148",

volume = "3",

pages = "855--870",

editor = "Mario Cannataro and Bruno Gaeta and {Asif Khan}, Mohammad",

booktitle = "Encyclopedia of bioinformatics and computational biology",

publisher = "Elsevier",

address = "Netherlands",

}

Identification of proteins from proteomic analysis. / Noor, Zainab; Mohamedali, Abidali ; Ranganathan, Shoba.
Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. ed. / Mario Cannataro; Bruno Gaeta; Mohammad Asif Khan. Vol. 3 Amsterdam; Oxford; Cambridge: Elsevier, 2019. p. 855-870.

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

TY - CHAP

T1 - Identification of proteins from proteomic analysis

AU - Noor, Zainab

AU - Mohamedali, Abidali

AU - Ranganathan, Shoba

N1 - Editors-in-chief: Shoba Ranganathan, Kenta Nakai, Christian Schönbach, Michael Gribskov.

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Proteomics data analysis

KW - Protein identification

KW - Tandem mass spectrometry

KW - Databases

KW - Trans-Proteomic pipeline

KW - Data processing

KW - Shotgun proteomics

KW - Protein annotation

KW - Web resources

UR - http://www.scopus.com/inward/record.url?scp=85079757043&partnerID=8YFLogxK

U2 - 10.1016/B978-0-12-809633-8.20478-0

DO - 10.1016/B978-0-12-809633-8.20478-0

M3 - Entry for encyclopedia/dictionary/reference book

SN - 9780128114148

VL - 3

SP - 855

EP - 870

BT - Encyclopedia of bioinformatics and computational biology

A2 - Cannataro, Mario

A2 - Gaeta, Bruno

A2 - Asif Khan, Mohammad

PB - Elsevier

CY - Amsterdam; Oxford; Cambridge

ER -

Identification of proteins from proteomic analysis

Abstract

Bibliographical note

Keywords

Access to Document

Other files and links

Fingerprint

Cite this