Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide

A. Kertesz-Farkas; F. L. Acquaye; V. Ostapenko; Rufino Haroldo Locon; Lu Y.; Grant C.; Noble W. S.

doi:10.1021/acs.jproteome.5c00297

Публикации

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Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide

Journal of Proteome Research. 2025. Vol. 24. No. 9. P. 4831–4837.

Кертес-Фаркаш А., Аквей Ф. Л., Остапенко В. Р., Rufino Haroldo Locon, Lu Y., Grant C., Noble W. S.

Научное направление: Химия

Язык: английский

DOI

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Ключевые слова: Database search tandem mass spectrometry peptide detection

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Rational design of gold-based nanocarriers for neurotherapeutics requires atomic-scale understanding of drug-material interactions. Density functional theory calculations were performed to investigate levodopa (L-DOPA) adsorption on small gold clusters (Au2–Au4) with cationic, neutral, and anionic charges, with additional validation on a larger Au10 cluster using multiple low-energy isomers. Binding free energies (ΔGbind), charge transfer, and electronic descriptors ...

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The first step in the analysis of protein tandem mass spectrometry data typically involves searching the observed spectra against a protein database. During database search, the search engine must digest the proteins in the database into peptides, subject to digestion rules that are under user control. The choice of these digestion parameters, as well as ...

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Spectrum annotation is a challenging task due to the presence of unexpected peptide fragmentation ions as well as the inaccuracy of the detectors of the spectrometers. We present a deep convolutional neural network, called Slider, which learns an optimal feature extraction in its kernels for scoring mass spectrometry (MS)/MS spectra to increase the number of ...

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Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LCMS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically ...

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