ArticleJournal of proteome research2020
Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- A porcine spectral assay library to quantify brain proteome by DIA-MS.Scientific data · 2026Article
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- Mass Spectrometry-Based Oral Meta-Omics Analysis-What We Know and What We Don't.Advances in experimental medicine and biology · 2026Review
- Tear fluid proteomics: a comparative study of DIA and DDA mass spectrometry.Journal of mass spectrometry and advances in the clinical lab · 2025Article
- Optimization of Methods for the Quantitative Analysis of Global Cell Surface Proteome and Cell Surface Polarization.International journal of molecular sciences · 2025Article
- Koina: Democratizing machine learning for proteomics research.Nature communications · 2025Article
- New Method Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data.Journal of proteome research · 2025Article
- Detection and Quantitation of Small Proteins Using Mass Spectrometry.Molecular & cellular proteomics : MCP · 2025Article
- The impact of exercise on skeletal muscle proteome of prediabetic subjects analyzed with data independent mass spectrometry.Scientific reports · 2025Article
- Proteomics in pancreatic cancer.Biomarker research · 2025Review
- Review
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Comparative Analysis of Protein Extraction Protocols for Olive Leaf Proteomics: Insights into Differential Protein Abundance and Isoelectric Point Distribution.ACS agricultural science & technology · 2025Article
- Recombinant Protein Spectral Library (rPSL) DIA-MS method improves identification and quantification of low-abundance cancer-associated and kynurenine pathway proteins.Communications chemistry · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- Multiplexed phosphoproteomics of low cell numbers using SPARCE.Communications biology · 2025Article
- Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis.Scientific reports · 2025Article
- Quantification of Peptides in Food Hydrolysate fromFoods (Basel, Switzerland) · 2025Article
2 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
Data-independent acquisition (DIA) is a promising technique for the proteomic analysis of complex protein samples. A number of studies have claimed that DIA experiments are more reproducible than data-dependent acquisition (DDA), but these claims are unsubstantiated since different data analysis methods are used in the two methods. Data analysis in most DIA workflows depends on spectral library searches, whereas DDA typically employs sequence database searches. In this study, we examined the reproducibility of the DIA and DDA results using both sequence database and spectral library search. The comparison was first performed using a cell lysate and then extended to an interactome study. Protein overlap among the technical replicates in both DDA and DIA experiments was 30% higher with library-based identifications than with sequence database identifications. The reproducibility of quantification was also improved with library search compared to database search, with the mean of the coefficient of variation decreasing more than 30% and a reduction in the number of missing values of more than 35%. Our results show that regardless of the acquisition method, higher identification and quantification reproducibility is observed when library search was used.
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