Human Prestin: a candidate PE1 protein lacking stringent mass spectrometric evidence?

Research output: Contribution to journalArticleResearchpeer-review

Abstract

The evidence that any protein exists in the Human Proteome Project (HPP; protein evidence 1 or PE1) has revolved primarily (although not exclusively) around mass spectrometry (MS) (93% of PE1 proteins have MS evidence in the latest neXtProt release), with robust and stringent, well-curated metrics that have served the community well. This has led to a significant number of proteins still considered "missing" (i.e., PE2-4). Many PE2-4 proteins have MS evidence of unacceptable quality (small or not enough unitypic peptides and unacceptably high protein/peptide FDRs), transcriptomic, or antibody evidence. Here we use a Chromosome 7 PE2 example called Prestin to demonstrate that clear and robust criteria/metrics need to be developed for proteins that may not or cannot produce clear-cut MS evidence while possessing significant non-MS evidence, including disease-association data. Many of the PE2-4 proteins are inaccessible, spatiotemporally expressed in a limited way, or expressed at such a very low copy number as to be unable to be detected by current MS methodologies. We propose that the HPP community consider and lead a communal initiative to accelerate the discovery and characterization of these types of "missing" proteins.

LanguageEnglish
Pages4531-4535
Number of pages5
JournalJournal of Proteome Research
Volume16
Issue number12
Early online date21 Sep 2017
DOIs
Publication statusPublished - 1 Dec 2017

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Mass spectrometry
Mass Spectrometry
Proteins
Peptides
Chromosomes, Human, Pair 7
Proteome
Chromosomes
Spectrometry
Spectrum Analysis
Antibodies
N-(4'-fluorobutyrophenone)-4-(4-chlorophenyl)pyridinium

Cite this

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title = "Human Prestin: a candidate PE1 protein lacking stringent mass spectrometric evidence?",
abstract = "The evidence that any protein exists in the Human Proteome Project (HPP; protein evidence 1 or PE1) has revolved primarily (although not exclusively) around mass spectrometry (MS) (93{\%} of PE1 proteins have MS evidence in the latest neXtProt release), with robust and stringent, well-curated metrics that have served the community well. This has led to a significant number of proteins still considered {"}missing{"} (i.e., PE2-4). Many PE2-4 proteins have MS evidence of unacceptable quality (small or not enough unitypic peptides and unacceptably high protein/peptide FDRs), transcriptomic, or antibody evidence. Here we use a Chromosome 7 PE2 example called Prestin to demonstrate that clear and robust criteria/metrics need to be developed for proteins that may not or cannot produce clear-cut MS evidence while possessing significant non-MS evidence, including disease-association data. Many of the PE2-4 proteins are inaccessible, spatiotemporally expressed in a limited way, or expressed at such a very low copy number as to be unable to be detected by current MS methodologies. We propose that the HPP community consider and lead a communal initiative to accelerate the discovery and characterization of these types of {"}missing{"} proteins.",
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Human Prestin : a candidate PE1 protein lacking stringent mass spectrometric evidence? / Mohamedali, Abidali; Ahn, Seong Beom; Sreenivasan, Varun K.A.; Ranganathan, Shoba; Baker, Mark S.

In: Journal of Proteome Research, Vol. 16, No. 12, 01.12.2017, p. 4531-4535.

Research output: Contribution to journalArticleResearchpeer-review

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