Deducing the presence of proteins and proteoforms in quantitative proteomics

Casimir Bamberger, Salvador Martínez-Bartolomé, Miranda Montgomery, Sandra Pankow, John D. Hulleman, Jeffery W. Kelly, John R. Yates

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The human genome harbors just 20,000 genes suggesting that the variety of possible protein products per gene plays a significant role in generating functional diversity. In bottom-up proteomics peptides are mapped back to proteins and proteoforms to describe a proteome; however, accurate quantitation of proteoforms is challenging due to incomplete protein sequence coverage and mapping ambiguities. Here, we demonstrate that a new software tool called ProteinClusterQuant (PCQ) can be used to deduce the presence of proteoforms that would have otherwise been missed, as exemplified in a proteomic comparison of two fly species, Drosophila melanogaster and D. virilis. PCQ was used to identify reduced levels of serine/threonine protein kinases PKN1 and PKN4 in CFBE41o- cells compared to HBE41o- cells and to elucidate that shorter proteoforms of full-length caspase-4 and ephrin B receptor are differentially expressed. Thus, PCQ extends current analyses in quantitative proteomics and facilitates finding differentially regulated proteins and proteoforms.

Original languageEnglish (US)
Article number2320
JournalNature Communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018

Fingerprint

Proteomics
proteins
Genes
Proteins
genes
Eph Family Receptors
proteome
Protein-Serine-Threonine Kinases
Human Genome
Drosophila
Proteome
Caspases
Ports and harbors
Drosophila melanogaster
Diptera
software development tools
harbors
genome
cells
Software

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Bamberger, C., Martínez-Bartolomé, S., Montgomery, M., Pankow, S., Hulleman, J. D., Kelly, J. W., & Yates, J. R. (2018). Deducing the presence of proteins and proteoforms in quantitative proteomics. Nature Communications, 9(1), [2320]. https://doi.org/10.1038/s41467-018-04411-5

Deducing the presence of proteins and proteoforms in quantitative proteomics. / Bamberger, Casimir; Martínez-Bartolomé, Salvador; Montgomery, Miranda; Pankow, Sandra; Hulleman, John D.; Kelly, Jeffery W.; Yates, John R.

In: Nature Communications, Vol. 9, No. 1, 2320, 01.12.2018.

Research output: Contribution to journalArticle

Bamberger, C, Martínez-Bartolomé, S, Montgomery, M, Pankow, S, Hulleman, JD, Kelly, JW & Yates, JR 2018, 'Deducing the presence of proteins and proteoforms in quantitative proteomics', Nature Communications, vol. 9, no. 1, 2320. https://doi.org/10.1038/s41467-018-04411-5
Bamberger C, Martínez-Bartolomé S, Montgomery M, Pankow S, Hulleman JD, Kelly JW et al. Deducing the presence of proteins and proteoforms in quantitative proteomics. Nature Communications. 2018 Dec 1;9(1). 2320. https://doi.org/10.1038/s41467-018-04411-5
Bamberger, Casimir ; Martínez-Bartolomé, Salvador ; Montgomery, Miranda ; Pankow, Sandra ; Hulleman, John D. ; Kelly, Jeffery W. ; Yates, John R. / Deducing the presence of proteins and proteoforms in quantitative proteomics. In: Nature Communications. 2018 ; Vol. 9, No. 1.
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