ArticleJournal of proteome research2022
Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
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Who cites it
168 citing papers in PubMed.
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- Quinoa and Peanut Extracts as Alternatives to Animal-Derived Extracellular Matrix Proteins in Cultured Meat Production.Journal of food science · 2026Article
- Palaeoproteomic Deconvolution of Physical and Genetic Collagen Mixtures.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cellular redox status is linked to olfactory alterations in cognitive decline.Redox biology · 2026Article
- B cell receptor-associated protein 31 levels in serum-derived extracellular vesicles are associated with therapeutic response and prognosis in patients with advanced hepatocellular carcinoma receiving atezolizumab plus bevacizumab: a multicenter study.Journal of gastroenterology · 2026Article
- Democratized single-cell proteomics resolves cell state heterogeneity in skin tumors.Life science alliance · 2026Article
- Reelin level in serum-derived extracellular vesicles predicts regression of M2BPGi-defined liver fibrosis following hepatitis C virus eradication by direct-acting antiviral agents.Journal of gastroenterology · 2026Article
- Cyclopropanol can function as a caged dual-functional warhead for selective electrochemical bioconjugation.Nature chemistry · 2026Article
- A porcine spectral assay library to quantify brain proteome by DIA-MS.Scientific data · 2026Article
- Brain metastasis-associated fibroblasts shape the tumour microenvironment to enhance cancer cell invasion.Brain pathology (Zurich, Switzerland) · 2026Article
- AURORA A interacts with DICER and SETD2 to promote S-phase progression.EMBO reports · 2026Article
- Microcephaly-like phenotype triggered by novel reassortant and prototypic Oropouche virus strains in brain organoids.EBioMedicine · 2026Article
- Avidin is evolutionarily conserved in fish but dispensable for development and resistance against Streptococcus agalactiae in zebrafish.FEBS open bio · 2026Article
108 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Mass spectrometry-based proteomics is constantly challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are almost impossible to avoid. For data-dependent acquisition (DDA) proteomics, an exclusion list can be used to reduce the influence of protein contaminants. However, protein contamination has not been evaluated and is rarely addressed in data-independent acquisition (DIA). How protein contaminants influence proteomic data is also unclear. In this study, we established new protein contaminant FASTA and spectral libraries that are applicable to all proteomic workflows and evaluated the impact of protein contaminants on both DDA and DIA proteomics. We demonstrated that including our contaminant libraries can reduce false discoveries and increase protein identifications, without influencing the quantification accuracy in various proteomic software platforms. With the pressing need to standardize proteomic workflow in the research community, we highly recommend including our contaminant FASTA and spectral libraries in all bottom-up proteomic data analysis. Our contaminant libraries and a step-by-step tutorial to incorporate these libraries in various DDA and DIA data analysis platforms can be valuable resources for proteomic researchers, freely accessible at https://github.com/HaoGroup-ProtContLib.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.