Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics

Sha Tian; Dongdong Zhan; Ying Yu; Yunzhi Wang; Mingwei Liu; Subei Tan; Yan Li; Lei Song; Zhaoyu Qin; Xianju Li; Yang Liu; Yao Li; Shuhui Ji; Shanshan Wang; Qing‐Yu He; Xingfeng Yin; Lunzhi Dai; Haiteng Deng; Chao Peng; Ping Wu; Minjia Tan; Jing Jiang; Yaoyang Zhang; Yunxia Li; Wenqin Liu; Wei Chen; Rui Wang; Jin Zi; Qidan Li; Mingzhou Bai

doi:10.1186/s13059-023-03048-y

Molecular BiologyGenome biologySep 6, 2023

Peer-reviewed journal article

Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics

Sha Tian iD, Dongdong Zhan iD, Ying Yu iD, Yunzhi Wang iD, Mingwei Liu iD, Subei Tan iD, Yan Li iD, Lei Song iD, Zhaoyu Qin iD, Xianju Li iD, Yang Liu iD, Yao Li iD, Shuhui Ji iD, Shanshan Wang iD, Qing‐Yu He iD, Xingfeng Yin, Lunzhi Dai iD, Haiteng Deng iD, Chao Peng iD, Ping Wu iD, Minjia Tan iD, Jing Jiang iD, Yaoyang Zhang iD, Yunxia Li iD, Wenqin Liu iD, , Chen Ding iD

Abstract

Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based measurements among different instruments and laboratories. We developed the Quartet as a proteome reference material with built-in truths, and distributed the same aliquots to 15 laboratories with nine conventional LC-MS/MS platforms across six cities in China. Relative abundance of over 12,000 proteins on 816 MS files were obtained and compared for reproducibility among the instruments and laboratories to ultimately generate proteomics benchmark datasets. There was a wide dynamic range of proteomes spanning ~7 orders of magnitude (101-108 copies/cell), and the injection order had marked effects on quantitative instead of qualitative. Overall, the Quartet offers valuable standard materials and data resources for improving the quality control of proteomic analyses as well as the reproducibility and reliability of research findings.

PDF DOI