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Tandem Mass Spectrometry

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Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry.

Nature communications
Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits t...

Deep learning neural network tools for proteomics.

Cell reports methods
Mass-spectrometry-based proteomics enables quantitative analysis of thousands of human proteins. However, experimental and computational challenges restrict progress in the field. This review summarizes the recent flurry of machine-learning strategie...

Pure Ion Chromatograms Combined with Advanced Machine Learning Methods Improve Accuracy of Discriminant Models in LC-MS-Based Untargeted Metabolomics.

Molecules (Basel, Switzerland)
Untargeted metabolomics based on liquid chromatography coupled with mass spectrometry (LC-MS) can detect thousands of features in samples and produce highly complex datasets. The accurate extraction of meaningful features and the building of discrimi...

pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning.

Journal of proteome research
In cross-linking mass spectrometry, the identification of cross-linked peptide pairs heavily relies on the ability of a database search engine to measure the similarities between experimental and theoretical MS/MS spectra. However, the lack of accura...

SteroidXtract: Deep Learning-Based Pattern Recognition Enables Comprehensive and Rapid Extraction of Steroid-Like Metabolic Features for Automated Biology-Driven Metabolomics.

Analytical chemistry
Despite the vast amount of metabolic information that can be captured in untargeted metabolomics, many biological applications are looking for a biology-driven metabolomics platform that targets a set of metabolites that are relevant to the given bio...

Pharmacokinetics of Eltrombopag in Healthy Chinese Subjects and Effect of Sex and Genetic Polymorphism on its Pharmacokinetic and Pharmacodynamic Variability.

European journal of drug metabolism and pharmacokinetics
BACKGROUND AND OBJECTIVE: Eltrombopag is the first oral, small-molecule, non-peptide thrombopoietin receptor agonist for the treatment of idiopathic thrombocytopenic purpura. This study investigated the pharmacokinetics of eltrombopag in healthy Chin...

Machine Learning Identifies Metabolic Signatures that Predict the Risk of Recurrent Angina in Remitted Patients after Percutaneous Coronary Intervention: A Multicenter Prospective Cohort Study.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Recurrent angina (RA) after percutaneous coronary intervention (PCI) has few known risk factors, hampering the identification of high-risk populations. In this multicenter study, plasma samples are collected from patients with stable angina after PCI...

Deep learning the collisional cross sections of the peptide universe from a million experimental values.

Nature communications
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million dat...

Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy.

BMC bioinformatics
BACKGROUND: Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in cancer cells lead to tumor r...

Simultaneous determination and quantitation of hypolipidemic drugs in fingerprints by UPLC-Q-TRAP/MS.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences
An ultra-performance liquid chromatography tandem triple quadrupole compound linear ion trap mass spectrometry (UPLC-Q-TRAP/MS) method was developed and validated for the detection of hypolipidemic drugs in fingerprints. 13 hypolipidemic drugs were w...