Recent Developments in Machine Learning for Mass Spectrometry

Recent Developments in Machine Learning for Mass Spectrometry

February 21, 2024 | Armen G. Beck, Matthew Muhoberac, Caitlin E. Randolph, Connor H. Beveridge, Prageeth R. Wijewardhane, Hilkka I. Kenttämaa, and Gaurav Chopra
The article "Recent Developments in Machine Learning for Mass Spectrometry" by Armen G. Beck et al. provides an overview of the integration of machine learning (ML) techniques with mass spectrometry (MS) data analysis. The authors highlight the historical and recent advancements in statistical and chemometric methods for MS data interpretation, emphasizing the recent renaissance of ML due to advancements in computational hardware and the development of new algorithms for artificial neural networks (ANN) and deep learning architectures. They discuss the practical aspects of ML methodology relevant to MS, including preprocessing, feature extraction, and various ML models such as supervised and unsupervised learning, ensemble learning, regression models, support vector machines, tree-based models, and deep learning architectures like ANNs, CNNs, autoencoders, RNNs, and transformers. The article also reviews recent applications of ML in MS, including spectral preprocessing, compound identification, sample classification, and clinical diagnostics. Specific examples include deisotoping high-resolution mass spectrometry data, mass spectral denoising, peak annotation, elemental composition determination, structural prediction, and mass spectral prediction. Additionally, the authors discuss the use of ML in omics-based disciplines such as proteomics, metabolomics, genomics, transcriptomics, and lipidomics, as well as in single-cell mass spectrometry (SCMS) studies. Overall, the article emphasizes the versatility and utility of ML in addressing the challenges associated with MS data interpretation and its potential to enhance various MS-based applications.The article "Recent Developments in Machine Learning for Mass Spectrometry" by Armen G. Beck et al. provides an overview of the integration of machine learning (ML) techniques with mass spectrometry (MS) data analysis. The authors highlight the historical and recent advancements in statistical and chemometric methods for MS data interpretation, emphasizing the recent renaissance of ML due to advancements in computational hardware and the development of new algorithms for artificial neural networks (ANN) and deep learning architectures. They discuss the practical aspects of ML methodology relevant to MS, including preprocessing, feature extraction, and various ML models such as supervised and unsupervised learning, ensemble learning, regression models, support vector machines, tree-based models, and deep learning architectures like ANNs, CNNs, autoencoders, RNNs, and transformers. The article also reviews recent applications of ML in MS, including spectral preprocessing, compound identification, sample classification, and clinical diagnostics. Specific examples include deisotoping high-resolution mass spectrometry data, mass spectral denoising, peak annotation, elemental composition determination, structural prediction, and mass spectral prediction. Additionally, the authors discuss the use of ML in omics-based disciplines such as proteomics, metabolomics, genomics, transcriptomics, and lipidomics, as well as in single-cell mass spectrometry (SCMS) studies. Overall, the article emphasizes the versatility and utility of ML in addressing the challenges associated with MS data interpretation and its potential to enhance various MS-based applications.
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