ArticleJournal of proteome research2019
Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed.
- Liver molecular networks associated with drinking behavior in nonhuman primates.Alcohol, clinical & experimental research · 2025Article
- IsoBayes: a Bayesian approach for single-isoform proteomics inference.Bioinformatics (Oxford, England) · 2025Article
- BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1.Nucleic acids research · 2025Article
- Genetic control over biogenic crystal morphogenesis in zebrafish.Nature chemical biology · 2025Article
- Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Diversification of molecular pattern recognition in bacterial NLR-like proteins.Nature communications · 2024Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- A survey of experimental and computational identification of small proteins.Briefings in bioinformatics · 2024Review
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer.bioRxiv : the preprint server for biology · 2024Article
- Integrated multi-omics analysis of brain aging in female nonhuman primates reveals altered signaling pathways relevant to age-related disorders.Neurobiology of aging · 2023Article
- Global detection of human variants and isoforms by deep proteome sequencing.Nature biotechnology · 2023Article
- Article
- Overview and considerations in bottom-up proteomics.The Analyst · 2023Review
- Enhanced Proteomic Data Analysis with MetaMorpheus.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method.International journal of molecular sciences · 2022Article
- DecipheringMolecular omics · 2022Article
- A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis.Journal of proteome research · 2022Article
- Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes.Journal of proteome research · 2022Article
- Enhanced protein isoform characterization through long-read proteogenomics.Genome biology · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Peptides detected by tandem mass spectrometry (MS/MS) in bottom-up proteomics serve as proxies for the proteins expressed in the sample. Protein inference is a process routinely applied to these peptides to generate a plausible list of candidate protein identifications. The use of multiple proteases for parallel protein digestions expands sequence coverage, provides additional peptide identifications, and increases the probability of identifying peptides that are unique to a single protein, which are all valuable for protein inference. We have developed and implemented a multi-protease protein inference algorithm in MetaMorpheus, a bottom-up search software program, which incorporates the calculation of protease-specific
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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.