Deducing the presence of proteins and proteoforms in quantitative proteomics

Nat Commun. 2018 Jun 13;9(1):2320. doi: 10.1038/s41467-018-04411-5.

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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Line
  • Cystic Fibrosis Transmembrane Conductance Regulator / chemistry
  • Cystic Fibrosis Transmembrane Conductance Regulator / genetics
  • Drosophila / chemistry
  • Drosophila / genetics
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / genetics
  • Drosophila melanogaster / chemistry
  • Drosophila melanogaster / genetics
  • Humans
  • Protein Interaction Maps
  • Protein Isoforms / chemistry
  • Protein Isoforms / genetics
  • Protein-Serine-Threonine Kinases / chemistry
  • Protein-Serine-Threonine Kinases / genetics
  • Proteome / chemistry
  • Proteome / genetics
  • Proteomics / methods*
  • Proteomics / statistics & numerical data
  • Software
  • Species Specificity

Substances

  • CFTR protein, human
  • Drosophila Proteins
  • Protein Isoforms
  • Proteome
  • Cystic Fibrosis Transmembrane Conductance Regulator
  • Protein-Serine-Threonine Kinases