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, Zhaoyu Qin, 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, Zeng Wang, Zhanlong Mei, Zhongyi Cheng, Jun Zhu, Xuemei Wu, Xing Yang, Yue Zhou, Yuanting Zheng, Fuchu He, Jun Qin, Chen Ding
Abstract
BACKGROUND: 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. RESULTS: Here, we develop the Quartet standard as a proteome reference material with built-in truths, and distribute 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 mass spectrometry files are obtained and compared for reproducibility among the instruments and laboratories to ultimately generate proteomics benchmark datasets. There is a wide dynamic range of proteomes spanning about 7 orders of magnitude, and the injection order has marked effects on quantitative instead of qualitative characteristics. CONCLUSION: 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.