ArticleMolecular & cellular proteomics : MCP2020
Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition.
Article in Molecular & cellular proteomics : MCP, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 78 citations in OpenAlex.
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- Avidin is evolutionarily conserved in fish but dispensable for development and resistance against Streptococcus agalactiae in zebrafish.FEBS open bio · 2026Article
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- JUMPlion improves quantitative DIA proteomics through ion-level recovery of missing values.bioRxiv : the preprint server for biology · 2026Article
- A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics.BMC bioinformatics · 2025Article
- A Flexible End-to-End Automated Sample Preparation Workflow Enables Standardized and Scalable Bottom-up Proteomics.Analytical chemistry · 2025Article
- Article
- Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry.Journal of proteome research · 2025Article
- Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics.Journal of proteome research · 2025Article
- Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition.Journal of the American Society for Mass Spectrometry · 2025Article
- Control of Golgi- V-ATPase through Sac1-dependent co-regulation of PI(4)P and cholesterol.Nature communications · 2025Article
- Targeting the Opioid System in Cardiovascular Disease: Liver Proteomic and Lipid Profile Effects of Naloxone in Atherosclerosis.Biomedicines · 2025Article
- Mass Spectrometry-based Solutions for Single-cell Proteomics.Genomics, proteomics & bioinformatics · 2025Review
- DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis.Nature communications · 2025Article
- Affinity Purification Mass Spectrometry on the Orbitrap-Astral Mass Spectrometer Enables High-Throughput Protein-Protein Interaction Mapping.Journal of proteome research · 2025Article
- Lipids as key biomarkers in unravelling the pathophysiology of obesity-related metabolic dysregulation.Heliyon · 2025Article
- Arabidopsis conditional photosynthesis mutants abc1k1 and var2 accumulate partially processed thylakoid preproteins and are defective in chloroplast biogenesis.Communications biology · 2025Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2024Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In bottom-up, label-free discovery proteomics, biological samples are acquired in a data-dependent (DDA) or data-independent (DIA) manner, with peptide signals recorded in an intact (MS1) and fragmented (MS2) form. While DDA has only the MS1 space for quantification, DIA contains both MS1 and MS2 at high quantitative quality. DIA profiles of complex biological matrices such as tissues or cells can contain quantitative interferences, and the interferences at the MS1 and the MS2 signals are often independent. When comparing biological conditions, the interferences can compromise the detection of differential peptide or protein abundance and lead to false positive or false negative conclusions.We hypothesized that the combined use of MS1 and MS2 quantitative signals could improve our ability to detect differentially abundant proteins. Therefore, we developed a statistical procedure incorporating both MS1 and MS2 quantitative information of DIA. We benchmarked the performance of the MS1-MS2-combined method to the individual use of MS1 or MS2 in DIA using four previously published controlled mixtures, as well as in two previously unpublished controlled mixtures. In the majority of the comparisons, the combined method outperformed the individual use of MS1 or MS2. This was particularly true for comparisons with low fold changes, few replicates, and situations where MS1 and MS2 were of similar quality. When applied to a previously unpublished investigation of lung cancer, the MS1-MS2-combined method increased the coverage of known activated pathways.Since recent technological developments continue to increase the quality of MS1 signals (
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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.