Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics
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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.
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Self-citationMethylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing
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Self-citationSEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data
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Decentralized nanoparticle protein corona analysis may misconduct biomarker discovery
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The emerging role of high-throughput proteomics in advancing precision medicine
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Self-citationAkkour, K., Rafiullah, M., Alfadda, A. A., Alanazi, I. O., Masood, A., Joy, S. S., Al-Eidan, A. A., Alshehri, E., Bassi, A., Alhalal, H., et al. (2026) · Cells · doi:10.3390/cells15060498 · Cited by 2 · see citing works
Construction of RNA reference materials for improving the quantification of transcriptomic data
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Self-citationChen, Q., Guo, X., Wang, D., Zhao, J., Xu, Y. J., You, Y., Mai, Y., Duan, S., Liu, Y., Zhang, Y., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.15.676287 · Cited by 2 · see citing works
Self-citationXiang, Y., Du, X., Yang, H., Wang, P., Yin, B., Wang, Z., Wang, H., Liu, L., Zhang, H., Ren, Y., et al. (2026) · Molecular Psychiatry · doi:10.1038/s41380-026-03443-4 · Cited by 1 · see citing works
Self-citationPlasma titration provides a physical ruler for cross-platform proteomicsPreprint
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Self-citationInformation on metrological follow-up and the preanalytical phase of omic methods
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- Authors
- Tian, S., Zhan, D., Yu, Y., Wang, Y., Liu, M., Tan, S., Li, Y., Song, L., Qin, Z., Li, X., Liu, Y., Li, Y., Ji, S., Wang, S., Proteomic Massive Analysis and Quality Control Consortium, Qin, Z., He, Q., Yin, X., Dai, L., Deng, H., Peng, C., Wu, P., Tan, M., Jiang, J., Zhang, Y., Li, Y., Liu, W., Chen, W., Wang, R., Zi, J., Li, Q., Bai, M., Wang, Z., Mei, Z., Cheng, Z., Zhu, J., Wu, X., Yang, X., Zhou, Y., Zheng, Y., He, F., Qin, J., & Ding, C.
- Affiliations
- Fudan University (CN)
- Beijing Proteome Research Center (CN)
- Thermo Fisher Scientific (China) (CN)
- Shanghai Medical College of Fudan University (CN)
- Corresponding author
- Zheng, Yuanting
- He, Fuchu
- Qin, Jun
- Ding, Chen
- ORCID
- Tian, Sha
- Zhan, Dongdong
- Yu, Ying
- Wang, Yunzhi
- Liu, Mingwei
- Tan, Subei
- Li, Yan
- Song, Lei
- Li, Xianju
- Liu, Yang
- Li, Yao
- Ji, Shuhui
- Wang, Shanshan
- Dai, Lunzhi
- Deng, Haiteng
- Peng, Chao
- Wu, Ping
- Tan, Minjia
- Jiang, Jing
- Zhang, Yaoyang
- Li, Yunxia
- Liu, Wenqin
- Chen, Wei
- Wang, Rui
- Zi, Jin
- Bai, Mingzhou
- Wang, Zeng
- Mei, Zhanlong
- Cheng, Zhongyi
- Wu, Xuemei
- He, Fuchu
- Qin, Jun
- Ding, Chen
- Venue
- Genome Biology
- Published
- 2023-09-07
- Volume
- 24
- Issue
- 1
- Pages
- 202-202
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC10483797
- OpenAlex
- W4386470877
- Cited by
- 43
- References
- 70
- Citations by year
- 2026: 8 · 2025: 8 · 2024: 18 · 2023: 6 · 2022: 3
- FWCI
- 4.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
- Funders
- National key research and development program (2022YFA1303200, 2022YFA1303201, 2022YFA1303202, 2020YFE0201600, 2018YFE0201600, 2018YFE0201603, 2018YFA0507500, 2018YFA0507501, 2017YFA0505100, 2017YFA0505102, 2017YFA0505101, 2017YFC0908404, 2016YFA0502500)
- The National Natural Science Foundation of China (31972933, 31770886, 31700682)
- Program of Shanghai Academic/Technology Research Leader (22XD1420100)
- Shuguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission (19SG02)
- The Shanghai Municipal Science and Technology Major Project (2017SHZDZX01)
- The Major Project of Special Development Funds of Zhangjiang National Independent Innovation Demonstration Zone (ZJ2019-ZD-004)
- The Fudan Original Research Personalized Support Project
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- label-free quantitative proteomics, interlaboratory comparison
- MeSH terms
- Chromatography, Liquid, Reproducibility of Results, Proteome, Proteomics, Tandem Mass Spectrometry
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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