emPAI Calc-for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry

Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

Summary: emPAI Calc is an open-source web application for the estimation of protein abundance. It uses the correlation between the number of identified peptides and protein abundance in mass spectrometry-based proteomic experiments. The program is the first implementation of our previously reported emPAI algorithm; it calculates the emPAI from the protein identification results obtained by database search engines such as Mascot.™ Availability: http://empai.iab.keio.ac.jp/; http://empai.iab.keio.ac.jp/supplement.php Source codes are available under Mozilla Public License. Contact: y-ishi@ttck.keio.ac.jp Supplementary Information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)576-577
Number of pages2
JournalBioinformatics
Volume26
Issue number4
DOIs
StatePublished - Dec 22 2009
Externally publishedYes

Fingerprint

Liquid chromatography
Mass Spectrometry
Tandem Mass Spectrometry
Chromatography
Liquid Chromatography
Mass spectrometry
Liquid
Proteins
Protein
Search Engine
Proteomics
Licensure
Bioinformatics
Search engines
Web Application
Computational Biology
Peptides
Open Source
Availability
Databases

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

emPAI Calc-for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. / Shinoda, Kosaku; Tomita, Masaru; Ishihama, Yasushi.

In: Bioinformatics, Vol. 26, No. 4, 22.12.2009, p. 576-577.

Research output: Contribution to journalArticle

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