Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data

Anal Chem. 2016 Feb 16;88(4):1973-8. doi: 10.1021/acs.analchem.5b04148. Epub 2016 Jan 29.


Quantitative proteomics can provide rich information on changes in biological functions and processes. However, its accuracy is affected by the inherent information degeneration found in bottom-up proteomics. Therefore, the precise protein inference from identified peptides can be mistaken since an ad hoc rule is used for generating a list of protein groups that depends on both the sample type and the sampling depth. Herein, we propose an alternative approach for examining quantitative proteomic data which is peptide-centric instead of protein-centric. We discuss the feasibility of the peptide-centric approach which was tested on several quantitative proteomic data sets. We show that peptide-centric quantification has several advantages over protein level analysis: (1) it is more sensitive for sample segregation, (2) it avoids the issues associated with protein inference, and (3) it can retrieve significant peptides lost in protein-centric quantification for further downstream analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Molecular Sequence Data
  • Peptides / analysis*
  • Peptides / chemistry
  • Principal Component Analysis
  • Proteins / chemistry
  • Proteomics / methods*
  • Spectrometry, Mass, Electrospray Ionization


  • Peptides
  • Proteins