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Deducing the presence of proteins and proteoforms in quantitative proteomics

Author

Listed:
  • Casimir Bamberger

    (The Scripps Research Institute)

  • Salvador Martínez-Bartolomé

    (The Scripps Research Institute)

  • Miranda Montgomery

    (The Scripps Research Institute)

  • Sandra Pankow

    (The Scripps Research Institute)

  • John D. Hulleman

    (University of Texas Southwestern Medical Center)

  • Jeffery W. Kelly

    (The Scripps Research Institute)

  • John R. Yates

    (The Scripps Research Institute)

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.

Suggested Citation

  • Casimir Bamberger & Salvador Martínez-Bartolomé & Miranda Montgomery & Sandra Pankow & John D. Hulleman & Jeffery W. Kelly & John R. Yates, 2018. "Deducing the presence of proteins and proteoforms in quantitative proteomics," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04411-5
    DOI: 10.1038/s41467-018-04411-5
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