Looking for missing proteins

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Abstract

Proteins are important biological macromolecules critical for structure, function and regulation of cells and tissues. The human genome draft is available since 2003 but until now not all the coding genes have known protein products. Human Proteome Project (HPP) was launched in 2010 with the aim of mapping the entire human proteome. The HPP community has identified 88.62% of the coding genes as protein products. The remaining 11.38% of the proteins are missing. Since most of the missing proteins are membrane proteins, which might have clinical implications, therefore it is important to identify these proteins for utilizing their therapeutic potential. There are several technical challenges that make the missing protein (MP) identification through mass spectrometry (MS), a difficult task. In this article we discuss the challenges associated with MP identification and the possible solutions applied by the scientific community. In the absence of reliable MS evidence for the MPs, other important experimental methods must also be considered for which no guidelines have yet been devised by the HPP. The largest family among the missing proteins is the olfactory receptors (ORs), which comprises the superfamily of G-protein coupled receptors (GPCRs). There is, till date, no convincible MS evidence available, for a single human OR, although four ORs have been assigned protein-level evidence status, based entirely on orthogonal evidence. Hence, there are likely to be numerous other ORs, with non-MS evidence. Therefore, we have collated the available orthogonal evidence for 107 ORs from published literature. At the end of the article, we present a case study for tracking missing ORs from orthogonal evidence.
LanguageEnglish
Title of host publicationReference module in life sciences
EditorsBernard D. Roitberg, Paul D. Cotter, Brian Dixon, Antonio Giordano, Roberto Mayor, Sharman O'Neill, Francesca Pentimalli, Shoba Ranganathan, Susan T. Sharfstein, Ilio Vitale, Ken Wilson, Oscar Zaragoza, Huan-Xiang Zhou
PublisherElsevier
Pages1-15
Number of pages15
ISBN (Electronic)9780128096338
DOIs
Publication statusPublished - 2019

Fingerprint

Odorant Receptors
Proteome
Proteins
Mass Spectrometry
Human Genome
G-Protein-Coupled Receptors
Spectrum Analysis
Membrane Proteins
Guidelines
Genes

Keywords

  • Deorphanization
  • Disease association
  • ectopic expression
  • functional characterization
  • GPCRs
  • Human Proteome Project (HPP)
  • Missing proteins
  • olfactory receptors
  • Orthogonal evidence
  • Site-directed mutagenesis

Cite this

Jabeen, A., Mohamedali, A., & Ranganathan, S. (2019). Looking for missing proteins. In B. D. Roitberg, P. D. Cotter, B. Dixon, A. Giordano, R. Mayor, S. O'Neill, F. Pentimalli, S. Ranganathan, S. T. Sharfstein, I. Vitale, K. Wilson, O. Zaragoza, ... H-X. Zhou (Eds.), Reference module in life sciences (pp. 1-15). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.20167-2
Jabeen, Amara ; Mohamedali, Abidali ; Ranganathan, Shoba. / Looking for missing proteins. Reference module in life sciences. editor / Bernard D. Roitberg ; Paul D. Cotter ; Brian Dixon ; Antonio Giordano ; Roberto Mayor ; Sharman O'Neill ; Francesca Pentimalli ; Shoba Ranganathan ; Susan T. Sharfstein ; Ilio Vitale ; Ken Wilson ; Oscar Zaragoza ; Huan-Xiang Zhou. Elsevier, 2019. pp. 1-15
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Jabeen, A, Mohamedali, A & Ranganathan, S 2019, Looking for missing proteins. in BD Roitberg, PD Cotter, B Dixon, A Giordano, R Mayor, S O'Neill, F Pentimalli, S Ranganathan, ST Sharfstein, I Vitale, K Wilson, O Zaragoza & H-X Zhou (eds), Reference module in life sciences. Elsevier, pp. 1-15. https://doi.org/10.1016/B978-0-12-809633-8.20167-2

Looking for missing proteins. / Jabeen, Amara; Mohamedali, Abidali; Ranganathan, Shoba.

Reference module in life sciences. ed. / Bernard D. Roitberg; Paul D. Cotter; Brian Dixon; Antonio Giordano; Roberto Mayor; Sharman O'Neill; Francesca Pentimalli; Shoba Ranganathan; Susan T. Sharfstein; Ilio Vitale; Ken Wilson; Oscar Zaragoza; Huan-Xiang Zhou. Elsevier, 2019. p. 1-15.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

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T1 - Looking for missing proteins

AU - Jabeen, Amara

AU - Mohamedali, Abidali

AU - Ranganathan, Shoba

PY - 2019

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N2 - Proteins are important biological macromolecules critical for structure, function and regulation of cells and tissues. The human genome draft is available since 2003 but until now not all the coding genes have known protein products. Human Proteome Project (HPP) was launched in 2010 with the aim of mapping the entire human proteome. The HPP community has identified 88.62% of the coding genes as protein products. The remaining 11.38% of the proteins are missing. Since most of the missing proteins are membrane proteins, which might have clinical implications, therefore it is important to identify these proteins for utilizing their therapeutic potential. There are several technical challenges that make the missing protein (MP) identification through mass spectrometry (MS), a difficult task. In this article we discuss the challenges associated with MP identification and the possible solutions applied by the scientific community. In the absence of reliable MS evidence for the MPs, other important experimental methods must also be considered for which no guidelines have yet been devised by the HPP. The largest family among the missing proteins is the olfactory receptors (ORs), which comprises the superfamily of G-protein coupled receptors (GPCRs). There is, till date, no convincible MS evidence available, for a single human OR, although four ORs have been assigned protein-level evidence status, based entirely on orthogonal evidence. Hence, there are likely to be numerous other ORs, with non-MS evidence. Therefore, we have collated the available orthogonal evidence for 107 ORs from published literature. At the end of the article, we present a case study for tracking missing ORs from orthogonal evidence.

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KW - Deorphanization

KW - Disease association

KW - ectopic expression

KW - functional characterization

KW - GPCRs

KW - Human Proteome Project (HPP)

KW - Missing proteins

KW - olfactory receptors

KW - Orthogonal evidence

KW - Site-directed mutagenesis

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BT - Reference module in life sciences

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A2 - Cotter, Paul D.

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A2 - Giordano, Antonio

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A2 - Pentimalli, Francesca

A2 - Ranganathan, Shoba

A2 - Sharfstein, Susan T.

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A2 - Wilson, Ken

A2 - Zaragoza, Oscar

A2 - Zhou, Huan-Xiang

PB - Elsevier

ER -

Jabeen A, Mohamedali A, Ranganathan S. Looking for missing proteins. In Roitberg BD, Cotter PD, Dixon B, Giordano A, Mayor R, O'Neill S, Pentimalli F, Ranganathan S, Sharfstein ST, Vitale I, Wilson K, Zaragoza O, Zhou H-X, editors, Reference module in life sciences. Elsevier. 2019. p. 1-15 https://doi.org/10.1016/B978-0-12-809633-8.20167-2