A protein identification algorithm for tandem mass spectrometry by incorporating the abundance of mRNA into a binomial probability scoring model.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of proteomics"
DOI: 10.1016/j.jprot.2019.02.010
Abstract: Peptide-spectrum matches (PSM) scoring between the experimental and theoretical spectrum is a key step in the identification of proteins using mass spectrometry (MS)-based proteomics analyses. Efficient protein identification using MS/MS data remains a challenge. The… read more here.
Keywords: identification; abundance; protein identification; scoring model ... See more keywords
Rapid Denaturing Organic Digestion Method for Targeted Protein Identification and Characterization.
Sign Up to like & getrecommendations! Published in 2021 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.0c04143
Abstract: Bottom-up mass spectrometry-based protein analysis methods employing protease digestion are routinely used to identify and characterize proteins with high specificity and sensitivity. Method performance is generally measured by sequence coverage capability and the total number… read more here.
Keywords: denaturing organic; digestion; method; organic digestion ... See more keywords
Liquid Chromatographic and Mass Spectrometric Methods for Quantitative Proteomic Analysis from Single-Cell and Nanogram-Level Samples.
Sign Up to like & getrecommendations! Published in 2025 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.5c02808
Abstract: Liquid chromatography (LC) and mass spectrometry (MS) are two critical components in proteomics. Advances in methods for both LC and MS have significantly enhanced protein identification and quantifications of limited amounts of proteins, particularly at… read more here.
Keywords: single cell; nanogram level; cell; proteomic analysis ... See more keywords
Deep Learning Powers Protein Identification from Precursor MS Information.
Sign Up to like & getrecommendations! Published in 2024 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.4c00118
Abstract: Proteome analysis currently heavily relies on tandem mass spectrometry (MS/MS), which does not fully utilize MS1 features, as many precursors remain unselected for MS/MS fragmentation, especially in the cases of low abundance samples and wide… read more here.
Keywords: deep learning; learning powers; identification; protein identification ... See more keywords
Nanopore-Based Protein Identification.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.1c11758
Abstract: The implementation of a reliable, rapid, inexpensive, and simple method for whole-proteome identification would greatly benefit cell biology research and clinical medicine. Proteins are currently identified by cleaving them with proteases, detecting the polypeptide fragments… read more here.
Keywords: identification; polypeptide fragments; based protein; protein identification ... See more keywords
Mass spectrometry-based protein identification in proteomics - a review
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbz163
Abstract: Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent… read more here.
Keywords: mass spectrometry; biology; identification proteomics; identification ... See more keywords
Development of an MS Workflow Based on Combining Database Search Engines for Accurate Protein Identification and Its Validation to Identify the Serum Proteomic Profile in Female Stress Urinary Incontinence
Sign Up to like & getrecommendations! Published in 2020 at "BioMed Research International"
DOI: 10.1155/2020/8740468
Abstract: A critical stage of shotgun proteomics is database search, a process which attempts to match the experimental spectra to the theoretical one. Given the considerable time and effort spent in analysis, it is self-evident for… read more here.
Keywords: search; database search; stress urinary; protein identification ... See more keywords
Single-molecule protein identification by sub-nanopore sensors
Sign Up to like & getrecommendations! Published in 2017 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1005356
Abstract: Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single… read more here.
Keywords: protein; single molecule; sub; identification ... See more keywords
DrugFinder: Druggable Protein Identification Model Based on Pre-Trained Models and Evolutionary Information
Sign Up to like & getrecommendations! Published in 2023 at "Algorithms"
DOI: 10.3390/a16060263
Abstract: The identification of druggable proteins has always been the core of drug development. Traditional structure-based identification methods are time-consuming and costly. As a result, more and more researchers have shifted their attention to sequence-based methods… read more here.
Keywords: identification; model; druggable protein; pre trained ... See more keywords
Protein Identification Improvement in Complex Samples Using Higher Frequency MS Acquisition and PEAKS Software
Sign Up to like & getrecommendations! Published in 2025 at "Applied Sciences"
DOI: 10.3390/app15020666
Abstract: Protein identification in complex biological samples using the shotgun mode of LC-MS/MS is typically enhanced by employing longer LC columns and extended gradient times. However, improved identification rates can also be achieved by optimizing MS… read more here.
Keywords: samples using; complex samples; acquisition; identification ... See more keywords