ArticleNature methods2009
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
Article in Nature methods, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed.
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- Reference Materials for Improving Reliability of Multiomics Profiling.Phenomics (Cham, Switzerland) · 2024Review
- RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification.Bioinformatics (Oxford, England) · 2024Article
- Proteomic insights into mental health status: plasma markers in young adults.Translational psychiatry · 2024Article
- A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities.Nature communications · 2024Article
- Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens.Journal of proteome research · 2024Article
- Identification of CD38, CD97, and CD278 on the HIV surface using a novel flow virometry screening assay.Scientific reports · 2023Article
- Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment.Communications biology · 2023Article
- A multi-omics dataset of human transcriptome and proteome stable reference.Scientific data · 2023Article
- Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine.Molecular & cellular proteomics : MCP · 2023Review
- Quality Control-A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome.Biomolecules · 2023Article
79 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.
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