ArticleJournal of proteome research2015
Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
64 citing papers in PubMed.
- Plasma proteomics reveal SERPINA1 and CD59 as candidate biomarkers for COVID-19 severity stratification and prognosis prediction.Annals of medicine · 2026Article
- DiaReport: reproducible workflow for differential expression analysis and interactive reporting in DIA-based proteomics.Bioinformatics (Oxford, England) · 2026Article
- Article
- Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins.Marine biotechnology (New York, N.Y.) · 2026Article
- Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Tear fluid proteomics: a comparative study of DIA and DDA mass spectrometry.Journal of mass spectrometry and advances in the clinical lab · 2025Article
- Comparative evaluation of analytical methods for CSF proteomics.Clinical proteomics · 2025Article
- Serum proteomics identify biomarkers and pathogenesis of portopulmonary hypertension diagnosed based on echocardiography.Scientific reports · 2025Article
- A micro-costing study of mass-spectrometry based quantitative proteomics testing applied to the diagnostic pipeline of mitochondrial and other rare disorders.Orphanet journal of rare diseases · 2024Article
- Deep Plasma Proteomics with Data-Independent Acquisition: Clinical Study Protocol Optimization with a COVID-19 Cohort.Journal of proteome research · 2024Article
- A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer.Scientific data · 2024Article
- Effect of dynamic exclusion and the use of FAIMS, DIA and MALDI-mass spectrometry imaging with ion mobility on amyloid protein identification.Clinical proteomics · 2024Article
- Unveiling the power of proteomics in advancing tropical animal health and production.Tropical animal health and production · 2024Article
- Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine.Journal of proteome research · 2024Article
- Recent progress in mass spectrometry-based urinary proteomics.Clinical proteomics · 2024Review
- Proteomics-driven noninvasive screening of circulating serum protein panels for the early diagnosis of hepatocellular carcinoma.Nature communications · 2023Article
- Mass spectrometry in cerebrospinal fluid uncovers association of glycolysis biomarkers with Alzheimer's disease in a large clinical sample.Scientific reports · 2023Article
- Resistance prediction in high-grade serous ovarian carcinoma with neoadjuvant chemotherapy using data-independent acquisition proteomics and an ovary-specific spectral library.Molecular oncology · 2023Article
- Advances in proteomics: characterization of the innate immune system after birth and during inflammation.Frontiers in immunology · 2023Review
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The promises of data-independent acquisition (DIA) strategies are a comprehensive and reproducible digital qualitative and quantitative record of the proteins present in a sample. We developed a fast and robust DIA method for comprehensive mapping of the urinary proteome that enables large scale urine proteomics studies. Compared to a data-dependent acquisition (DDA) experiments, our DIA assay doubled the number of identified peptides and proteins per sample at half the coefficients of variation observed for DDA data (DIA = ∼8%; DDA = ∼16%). We also tested different spectral libraries and their effects on overall protein and peptide identifications and their reproducibilities, which provided clear evidence that sample type-specific spectral libraries are preferred for reliable data analysis. To show applicability for biomarker discovery experiments, we analyzed a sample set of 87 urine samples from children seen in the emergency department with abdominal pain. The whole set was analyzed with high proteome coverage (∼1300 proteins/sample) in less than 4 days. The data set revealed excellent biomarker candidates for ovarian cyst and urinary tract infection. The improved throughput and quantitative performance of our optimized DIA workflow allow for the efficient simultaneous discovery and verification of biomarker candidates without the requirement for an early bias toward selected proteins.
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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 OpenQuestion graph.