Identification of proteins from proteomic analysis

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary/reference book

1 Citation (Scopus)


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 languageEnglish
Title of host publicationEncyclopedia of bioinformatics and computational biology
Subtitle of host publicationABC of Bioinformatics
EditorsMario Cannataro, Bruno Gaeta, Mohammad Asif Khan
Place of PublicationAmsterdam; Oxford; Cambridge
Number of pages16
ISBN (Electronic)9780128114322
ISBN (Print)9780128114148
Publication statusPublished - 2019

Bibliographical note

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


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


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