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 journalArticlepeer-review

15 Scopus citations


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
Issue number1
StatePublished - Dec 1 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).


Dive into the research topics of 'Deducing the presence of proteins and proteoforms in quantitative proteomics'. Together they form a unique fingerprint.

Cite this