ArticleNature methods2018
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- DECAF: Deconvoluted Extracted Ion Chromatogram-Based Quantification of Therapeutic Oligonucleotides.Molecules (Basel, Switzerland) · 2026Article
- spatialstein: An Open-Source Workflow for Annotation, Deconvolution, and Spatially Aware Segmentation of Mass Spectrometry Imaging Data.Analytical chemistry · 2026Article
- Scoring information integration with statistical quality control enhanced cross-run analysis of data-independent acquisition proteomics data.Communications chemistry · 2025Article
- QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry-Based Proteomics Datasets.Proteomics · 2025Article
- Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment.Nature methods · 2025Article
- Increasing mass spectrometry throughput using time-encoded sample multiplexing.bioRxiv : the preprint server for biology · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis.Nature communications · 2025Article
- SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run.Journal of proteome research · 2025Article
- TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.Journal of proteome research · 2025Article
- An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software.Journal of the American Society for Mass Spectrometry · 2024Article
- SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics.Interdisciplinary sciences, computational life sciences · 2024Article
- Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2024Review
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping.Nature communications · 2024Article
- A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology.Biophysics reports · 2023Article
- Dear-DIAResearch (Washington, D.C.) · 2023Article
- Resolving isobaric interferences in direct infusion tandem mass spectrometry.Rapid communications in mass spectrometry : RCM · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Mass spectrometry with data-independent acquisition (DIA) is a promising method to improve the comprehensiveness and reproducibility of targeted and discovery proteomics, in theory by systematically measuring all peptide precursors in a biological sample. However, the analytical challenges involved in discriminating between peptides with similar sequences in convoluted spectra have limited its applicability in important cases, such as the detection of single-nucleotide polymorphisms (SNPs) and alternative site localizations in phosphoproteomics data. We report Specter (https://github.com/rpeckner-broad/Specter), an open-source software tool that uses linear algebra to deconvolute DIA mixture spectra directly through comparison to a spectral library, thus circumventing the problems associated with typical fragment-correlation-based approaches. We validate the sensitivity of Specter and its performance relative to that of other methods, and show that Specter is able to successfully analyze cases involving highly similar peptides that are typically challenging for DIA analysis methods.
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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.