ArticleMolecular & cellular proteomics : MCP2012
Protein identification using top-down.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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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
96 citing papers in PubMed.
- Integrating Spatial Proteogenomics in Cancer Research.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Automating Middle-Down Mass Spectrometry Analysis for Extensive Antibody Characterization.Analytical chemistry · 2026Article
- Top-Down Mass Spectrometry and Its Current Applications in Biomarker Discovery in Aging and Age-Related Diseases.International journal of molecular sciences · 2026Review
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- ResNeXt-Based Rescoring Model for Proteoform Characterization in Top-Down Mass Spectra.Interdisciplinary sciences, computational life sciences · 2025Article
- A Fast Neural Network for Isotopic Charge State Assignment.Journal of the American Chemical Society · 2025Article
- Deciphering Proteoform Landscape of Mammary Carcinoma by Top-Down Proteomics.Journal of proteome research · 2025Article
- FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.Journal of the American Society for Mass Spectrometry · 2025Article
- Improving Top-Down Sequence Coverage with Targeted Fragment Matching.Journal of the American Society for Mass Spectrometry · 2024Article
- MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data.Bioinformatics (Oxford, England) · 2024Article
- Spectral averaging with outlier rejection algorithms to increase identifications in top-down proteomics.Proteomics · 2024Article
- Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.Journal of proteome research · 2023Article
- MASH Native: a unified solution for native top-down proteomics data processing.Bioinformatics (Oxford, England) · 2023Article
- TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.Journal of proteome research · 2023Article
- Size Exclusion Chromatography Strategies and MASH Explorer for Large Proteoform Characterization.Methods in molecular biology (Clifton, N.J.) · 2022Article
- PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics.Nucleic acids research · 2021Article
- Novel Strategies to Address the Challenges in Top-Down Proteomics.Journal of the American Society for Mass Spectrometry · 2021Review
36 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set.
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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.