Artificial intelligence in molecular medicine

B Gomes, EA Ashley - New England Journal of Medicine, 2023‏ - Mass Medical Soc
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Artificial intelligence for proteomics and biomarker discovery

M Mann, C Kumar, WF Zeng, MT Strauss - Cell systems, 2021‏ - cell.com
There is an avalanche of biomedical data generation and a parallel expansion in
computational capabilities to analyze and make sense of these data. Starting with genome …

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

F Yu, GC Teo, AT Kong, K Fröhlich, GX Li… - Nature …, 2023‏ - nature.com
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

MSBooster: improving peptide identification rates using deep learning-based features

KL Yang, F Yu, GC Teo, K Li, V Demichev… - Nature …, 2023‏ - nature.com
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

WF Zeng, XX Zhou, S Willems, C Ammar… - Nature …, 2022‏ - nature.com
Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …

Data‐independent acquisition mass spectrometry‐based proteomics and software tools: a glimpse in 2020

F Zhang, W Ge, G Ruan, X Cai, T Guo - Proteomics, 2020‏ - Wiley Online Library
This review provides a brief overview of the development of data‐independent acquisition
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …

Prediction of peptide mass spectral libraries with machine learning

J Cox - Nature Biotechnology, 2023‏ - nature.com
The recent development of machine learning methods to identify peptides in complex mass
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …

[HTML][HTML] Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023

R Lou, W Shui - Molecular & Cellular Proteomics, 2024‏ - Elsevier
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …

Prediction of glycopeptide fragment mass spectra by deep learning

Y Yang, Q Fang - Nature Communications, 2024‏ - nature.com
Deep learning has achieved a notable success in mass spectrometry-based proteomics and
is now emerging in glycoproteomics. While various deep learning models can predict …

Deep learning in proteomics

B Wen, WF Zeng, Y Liao, Z Shi, SR Savage… - …, 2020‏ - Wiley Online Library
Proteomics, the study of all the proteins in biological systems, is becoming a data‐rich
science. Protein sequences and structures are comprehensively catalogued in online …