A Short Overview of the Components in Mass Spectrometry Instrumentation for Proteomics Analyses

Demartini, Diogo Ribeiro

doi:10.5772/54484

“…The identification of the structure of a chemical compound is perceived as one of the most time consuming and laborious task in chemical analysis. This is often performed through analytical techniques such as mass spectroscopy (MS) and nuclear magnetic resonance (NMR) [3,4,5] with MS being used more often due to its higher sensitivity and specificity [3]. In MS, the molecules that are present in a biological sample are first separated using a chromatographic technique, such as liquid chromatography (LC) and gas chromatography (GC), with the latter being used more commonly [1,6].…”

Section: Introductionmentioning

confidence: 99%

“…The information that is collected from this process is presented in the mass spectrum which is a graph with the m/z of each recorded fragment in the horizontal axis and the relative abundance in the vertical axis. In order to obtain more detailed information on the query structure, a sequential fragmentation process is often used called tandem mass spectrometry [5]. Once the molecule has been fragmented into ions, a set of them, called precursor ions, is selected and further fragmented to generate MS2 (also called MS/MS) spectra.…”

Section: Introductionmentioning

confidence: 99%

Spec2Mol: An end-to-end deep learning framework for translating MS/MS Spectra to de-novo molecules

Litsa

¹

,

Chenthamarakshan

²

,

Das

³

et al. 2021

Preprint

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Elucidating the structure of a chemical compound is a fundamental task in chemistry with application in multiple domains including the emerging field of metabolomics, with promising applications in drug discovery, precision medicine, and biomarker discovery. The common practice for elucidating the structure of a chemical compound is to obtain a mass spectrum and subsequently retrieve its structure from spectral databases. However, database retrieval methods fail to identify novel molecules that are not present in the reference database. In this work, we propose Spec2Mol, a deep learning architecture for molecular structure recommendation given mass spectra alone. Spec2Mol is inspired by the Speech2Text deep learning architectures for translating audio signals into text. Our approach is based on an encoder-decoder architecture. The encoder learns the spectra embeddings, while the decoder, pre-trained on a massive dataset of chemical structures for translating between different molecular representations, reconstructs SMILES sequences of the recommended chemical structures. We have evaluated Spec2Mol by assessing the molecular similarity between the recommended structures and the original structure. Our analysis showed that Spec2Mol is able to identify the presence of key substructures in the molecule from its mass spectrum, and shows on par performance, when compared to existing fragmentation tree based methods, in recommending molecules for a given mass spectrum.

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Spec2Mol: An end-to-end deep learning framework for translating MS/MS Spectra to de-novo molecules

Litsa

¹

,

Chenthamarakshan

²

,

Das

³

et al. 2021

Preprint

View full text Add to dashboard Cite

Elucidating the structure of a chemical compound is a fundamental task in chemistry with application in multiple domains including the emerging field of metabolomics, with promising applications in drug discovery, precision medicine, and biomarker discovery. The common practice for elucidating the structure of a chemical compound is to obtain a mass spectrum and subsequently retrieve its structure from spectral databases. However, database retrieval methods fail to identify novel molecules that are not present in the reference database. In this work, we propose Spec2Mol, a deep learning architecture for molecular structure recommendation given mass spectra alone. Spec2Mol is inspired by the Speech2Text deep learning architectures for translating audio signals into text. Our approach is based on an encoder-decoder architecture. The encoder learns the spectra embeddings, while the decoder, pre-trained on a massive dataset of chemical structures for translating between different molecular representations, reconstructs SMILES sequences of the recommended chemical structures. We have evaluated Spec2Mol by assessing the molecular similarity between the recommended structures and the original structure. Our analysis showed that Spec2Mol is able to identify the presence of key substructures in the molecule from its mass spectrum, and shows on par performance, when compared to existing fragmentation tree based methods, in recommending molecules for a given mass spectrum.

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Mass Spectrophotometry: An Advanced Technique in Biomedical Sciences

Paital¹

2015

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Present century is the era of life sciences and metabolomics is the dominating field in present day over genomics and proteomics. Powerful techniques in the later cases are useful to determine the qualitative and quantitative studies of the levels of metabolites in bio-medical samples. In past time, biochemistry had very least role because the analyses of metabolites using individual conventional biochemical techniques had been used from past centuries. Owing to this limitation, mass spectrometry (MS) was introduced in bio-medical sciences. The fundamental rule in MS is that it ionizes individual chemical species and sorts the fragmented samples at charged state (ions) on the basis of their mass to charge (m/z) ratio. Therefore, each molecule in purified form or in homogenate can be identified and quantified based on their unique m/z ratio. In other words, MS measures the masses of the fragmented samples by enabling them to be charged during measurement. This particular technique has therefore, many applications starting from quantitative to qualitative analyses of metabolites under normal, experimental and diseased conditions in organisms including human being. Based on the method applied, sample preparation process, sample type, measurement process such as abundance or time of retention or flight of charged fragments etc., each MS vary with its own advantages and disadvantages. A general commentary article is written on this particular modern technique to make it understood and popular among the researchers.

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A Short Overview of the Components in Mass Spectrometry Instrumentation for Proteomics Analyses

Cited by 3 publications

References 78 publications

Spec2Mol: An end-to-end deep learning framework for translating MS/MS Spectra to de-novo molecules

Spec2Mol: An end-to-end deep learning framework for translating MS/MS Spectra to de-novo molecules

Spec2Mol: An end-to-end deep learning framework for translating MS/MS Spectra to de-novo molecules

Mass Spectrophotometry: An Advanced Technique in Biomedical Sciences

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