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 and John R. Yates ()
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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

Nature Communications, 2018, vol. 9, issue 1, 1-12

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-04411-5

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