A reference peptide database for proteome quantification based on experimental mass spectrum response curves

Wanlin Liu, Lai Wei, Jianan Sun, Jinwen Feng, Gaigai Guo, Lizhu Liang, Tianyi Fu, Mingwei Liu, Kai Li, Yin Huang, Weimin Zhu, Bei Zhen (+4 others)
2018 Bioinformatics  
Motivation: Mass spectrometry (MS) based quantification of proteins/peptides has become a powerful tool in biological research with high sensitivity and throughput. The accuracy of quantification, however, has been problematic as not all peptides are suitable for quantification. Several methods and tools have been developed to identify peptides that response well in mass spectrometry and they are mainly based on predictive models, and rarely consider the linearity of the response curve,
more » ... the accuracy and applicability of the methods. An alternative solution is to select empirically superior peptides that offer satisfactory MS response intensity and linearity in a wide dynamic range of peptide concentration. Results: We constructed a reference database for proteome quantification based on experimental mass spectrum response curves. The intensity and dynamic range of over 2 647 773 transitions from 121 318 peptides were obtained from a set of dilution experiments, covering 11 040 gene products. These transitions and peptides were evaluated and presented in a database named SCRIPT-MAP. We showed that the best-responder (BR) peptide approach for quantification based on SCRIPT-MAP database is robust, repeatable and accurate in proteome-scale protein quantification. This study provides a reference database as well as a peptides/transitions selection method for quantitative proteomics.
doi:10.1093/bioinformatics/bty201 pmid:29617941 pmcid:PMC6084618 fatcat:w3xhljj6xzhplfsuypxbnxokh4