ArticleBioinformatics (Oxford, England)2021
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling.The EMBO journal · 2026Article
- Data-independent acquisition-based quantitative proteomics in plants.Frontiers in plant science · 2026Review
- A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data.Nature methods · 2025Article
- Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment.Nature methods · 2025Article
- Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.Proteomics · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- Enhanced Discovery of Alternative Proteins (AltProts) in Mouse Cardiac Development Using Data-Independent Acquisition (DIA) Proteomics.Analytical chemistry · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.Nature communications · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.bioRxiv : the preprint server for biology · 2024Article
- Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.Nature communications · 2023Article
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Proteomic Analysis of Human Follicular Fluid Reveals the Pharmacological Mechanisms of the Chinese Patent Drug Kunling Pill for Improving Diminished Ovarian Reserve.Evidence-based complementary and alternative medicine : eCAM · 2022Article
- Software Design and Analytical Challenges for Confident Glycopeptide Identification With Data-Independent Acquisition.Mass spectrometry reviewsReview
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Authors and funding
5 authors.
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Abstract
motivationTandem mass spectrometry data acquired using data independent acquisition (DIA) is challenging to interpret because the data exhibits complex structure along both the mass-to-charge (m/z) and time axes. The most common approach to analyzing this type of data makes use of a library of previously observed DIA data patterns (a 'spectral library'), but this approach is expensive because the libraries do not typically generalize well across laboratories.
resultsHere, we propose DIAmeter, a search engine that detects peptides in DIA data using only a peptide sequence database. Although some existing library-free DIA analysis methods (i) support data generated using both wide and narrow isolation windows, (ii) detect peptides containing post-translational modifications, (iii) analyze data from a variety of instrument platforms and (iv) are capable of detecting peptides even in the absence of detectable signal in the survey (MS1) scan, DIAmeter is the only method that offers all four capabilities in a single tool. AVAILABILITY AND IMPLEMENTATION: The open source, Apache licensed source code is available as part of the Crux mass spectrometry analysis toolkit (http://crux.ms). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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