AIMC Topic: Mass Spectrometry

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The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows.

Proteomics
A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include metaproteomics, proteogenomics, data independent acquisition (DIA), non-specific proteolysis, immunopeptidomics, and open ...

Single-Cell Classification Using Mass Spectrometry through Interpretable Machine Learning.

Analytical chemistry
The brain consists of organized ensembles of cells that exhibit distinct morphologies, cellular connectivity, and dynamic biochemistries that control the executive functions of an organism. However, the relationships between chemical heterogeneity, c...

Immunopeptidomic Data Integration to Artificial Neural Networks Enhances Protein-Drug Immunogenicity Prediction.

Frontiers in immunology
Recombinant DNA technology has, in the last decades, contributed to a vast expansion of the use of protein drugs as pharmaceutical agents. However, such biological drugs can lead to the formation of anti-drug antibodies (ADAs) that may result in adve...

How to Apply Supervised Machine Learning Tools to MS Imaging Files: Case Study with Cancer Spheroids Undergoing Treatment with the Monoclonal Antibody Cetuximab.

Journal of the American Society for Mass Spectrometry
As the field of mass spectrometry imaging continues to grow, so too do its needs for optimal methods of data analysis. One general need in image analysis is the ability to classify the underlying regions within an image, as healthy or diseased, for e...

PB-Net: Automatic peak integration by sequential deep learning for multiple reaction monitoring.

Journal of proteomics
Mass spectrometry (MS) based proteomics has become an indispensable component of modern molecular and cellular biochemistry analysis. Multiple reaction monitoring (MRM) is one of the most well-established MS techniques for molecule detection and quan...

EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-Spectral Deconvolution.

Analytical chemistry
Top-down mass spectrometry has become the main method for intact proteoform identification, characterization, and quantitation. Because of the complexity of top-down mass spectrometry data, spectral deconvolution is an indispensable step in spectral ...

NormAE: Deep Adversarial Learning Model to Remove Batch Effects in Liquid Chromatography Mass Spectrometry-Based Metabolomics Data.

Analytical chemistry
Untargeted metabolomics based on liquid chromatography-mass spectrometry is affected by nonlinear batch effects, which cover up biological effects, result in nonreproducibility, and are difficult to be calibrate. In this study, we propose a novel dee...

Identification of the Species Constituents of Maggot Populations Feeding on Decomposing Remains-Facilitation of the Determination of Post Mortem Interval and Time Since Tissue Infestation through Application of Machine Learning and Direct Analysis in Real Time-Mass Spectrometry.

Analytical chemistry
The utilization of entomological specimens such as larvae (maggots) for the estimation of time since oviposition (i.e., egg laying) for post mortem interval determination, or for estimation of time since tissue infestation (in investigations of elder...

Using isotopic envelopes and neural decision tree-based in silico fractionation for biomolecule classification.

Analytica chimica acta
Untargeted mass spectrometry (MS) workflows are more suitable than targeted workflows for high throughput characterization of complex biological samples. However, analysis workflows for untargeted methods are inadequate for characterization of comple...