RESUMEN
The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.
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Ácidos y Sales Biliares , Microbioma Gastrointestinal , Metabolómica , Espectrometría de Masas en Tándem , Animales , Humanos , Ácidos y Sales Biliares/química , Metabolómica/métodos , Poliaminas , Espectrometría de Masas en Tándem/métodos , Bases de Datos de Compuestos QuímicosRESUMEN
Computational methods that aim to exploit publicly available mass spectrometry repositories rely primarily on unsupervised clustering of spectra. Here we trained a deep neural network in a supervised fashion on the basis of previous assignments of peptides to spectra. The network, called 'GLEAMS', learns to embed spectra in a low-dimensional space in which spectra generated by the same peptide are close to one another. We applied GLEAMS for large-scale spectrum clustering, detecting groups of unidentified, proximal spectra representing the same peptide. We used these clusters to explore the dark proteome of repeatedly observed yet consistently unidentified mass spectra.
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Péptidos , Espectrometría de Masas en Tándem , Algoritmos , Análisis por Conglomerados , Redes Neurales de la Computación , Péptidos/química , Proteoma/análisis , Espectrometría de Masas en Tándem/métodosRESUMEN
Immunopeptidomics is a key technology in the discovery of targets for immunotherapy and vaccine development. However, identifying immunopeptides remains challenging due to their non-tryptic nature, which results in distinct spectral characteristics. Moreover, the absence of strict digestion rules leads to extensive search spaces, further amplified by the incorporation of somatic mutations, pathogen genomes, unannotated open reading frames, and post-translational modifications. This inflation in search space leads to an increase in random high-scoring matches, resulting in fewer identifications at a given false discovery rate. Peptide-spectrum match rescoring has emerged as a machine learning-based solution to address challenges in mass spectrometry-based immunopeptidomics data analysis. It involves post-processing unfiltered spectrum annotations to better distinguish between correct and incorrect peptide-spectrum matches. Recently, features based on predicted peptidoform properties, including fragment ion intensities, retention time, and collisional cross section, have been used to improve the accuracy and sensitivity of immunopeptide identification. In this review, we describe the diverse bioinformatics pipelines that are currently available for peptide-spectrum match rescoring and discuss how they can be used for the analysis of immunopeptidomics data. Finally, we provide insights into current and future machine learning solutions to boost immunopeptide identification.
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Péptidos , Proteómica , Proteómica/métodos , Péptidos/química , Espectrometría de Masas/métodos , Aprendizaje Automático , Procesamiento Proteico-PostraduccionalRESUMEN
Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USI enables greater transparency of spectral evidence, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.
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Bases de Datos de Proteínas , Espectrometría de Masas/métodos , Proteómica/métodos , Procesamiento de Señales Asistido por Computador , Programas Informáticos , AlgoritmosRESUMEN
MOTIVATION: Driven by technological advances, the throughput and cost of mass spectrometry (MS) proteomics experiments have improved by orders of magnitude in recent decades. Spectral library searching is a common approach to annotating experimental mass spectra by matching them against large libraries of reference spectra corresponding to known peptides. An important disadvantage, however, is that only peptides included in the spectral library can be found, whereas novel peptides, such as those with unexpected post-translational modifications (PTMs), will remain unknown. Open modification searching (OMS) is an increasingly popular approach to annotate modified peptides based on partial matches against their unmodified counterparts. Unfortunately, this leads to very large search spaces and excessive runtimes, which is especially problematic considering the continuously increasing sizes of MS proteomics datasets. RESULTS: We propose an OMS algorithm, called HOMS-TC, that fully exploits parallelism in the entire pipeline of spectral library searching. We designed a new highly parallel encoding method based on the principle of hyperdimensional computing to encode mass spectral data to hypervectors while minimizing information loss. This process can be easily parallelized since each dimension is calculated independently. HOMS-TC processes two stages of existing cascade search in parallel and selects the most similar spectra while considering PTMs. We accelerate HOMS-TC on NVIDIA's tensor core units, which is emerging and readily available in the recent graphics processing unit (GPU). Our evaluation shows that HOMS-TC is 31× faster on average than alternative search engines and provides comparable accuracy to competing search tools. AVAILABILITY AND IMPLEMENTATION: HOMS-TC is freely available under the Apache 2.0 license as an open-source software project at https://github.com/tycheyoung/homs-tc.
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Programas Informáticos , Espectrometría de Masas en Tándem , Espectrometría de Masas en Tándem/métodos , Bases de Datos de Proteínas , Péptidos/química , Motor de Búsqueda , Algoritmos , Biblioteca de PéptidosRESUMEN
Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between closely related aneuploid strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, as in other Eukaryotes, we observed attenuation of dosage effects for protein complex subunits and in addition, non-cytoplasmic proteins. Differentially expressed transcripts and proteins between aneuploid Leishmania strains also originated from non-aneuploid chromosomes. At protein level, these were enriched for proteins involved in protein metabolism, such as chaperones and chaperonins, peptidases, and heat-shock proteins. In conclusion, our results further support the view that aneuploidy in Leishmania can be adaptive. Additionally, we believe that the high karyotype diversity in vitro and absence of classical transcriptional regulation make Leishmania an attractive model to study processes of protein homeostasis in the context of aneuploidy and beyond.
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Leishmania donovani , Proteoma , Aneuploidia , Proteínas de Choque Térmico/genética , Humanos , Cariotipo , Leishmania donovani/genética , Péptido Hidrolasas/genética , Proteoma/genéticaRESUMEN
Predicting drug toxicity is a critical aspect of ensuring patient safety during the drug design process. Although conventional machine learning techniques have shown some success in this field, the scarcity of annotated toxicity data poses a significant challenge in enhancing models' performance. In this study, we explore the potential of leveraging large unlabeled small molecule data sets using semisupervised learning to improve drug cardiotoxicity predictive performance across three cardiac ion channel targets: the voltage-gated potassium channel (hERG), the voltage-gated sodium channel (Nav1.5), and the voltage-gated calcium channel (Cav1.2). We extensively mined the ChEMBL database, comprising approximately 2 million small molecules, and then employed semisupervised learning to construct robust classification models for this purpose. We achieved a performance boost on highly diverse (i.e., structurally dissimilar) test data sets across all three targets. Using our built models, we screened the whole ChEMBL database and a large set of FDA-approved drugs, identifying several compounds with potential cardiac ion channel activity. To ensure broad accessibility and usability for both technical and nontechnical users, we developed a cross-platform graphical user interface that allows users to make predictions and gain insights into the cardiotoxicity of drugs and other small molecules. The software is made available as open source under the permissive MIT license at https://github.com/issararab/CToxPred2.
RESUMEN
In the field of drug discovery, there is a substantial challenge in seeking out chemical structures that possess desirable pharmacological, toxicological, and pharmacokinetic properties. Complications arise when drugs interfere with the functioning of cardiac ion channels, leading to serious cardiovascular consequences. The discontinuation and removal of numerous approved drugs from the market or at late development stages in the pipeline due to such inhibitory effects further highlight the urgency of addressing this issue. Consequently, the early prediction of potential blockers targeting cardiac ion channels during the drug discovery process is of paramount importance. This study introduces a deep learning framework that computationally determines the cardiotoxicity associated with the voltage-gated potassium channel (hERG), the voltage-gated calcium channel (Cav1.2), and the voltage-gated sodium channel (Nav1.5) for drug candidates. The predictive capabilities of three feature representationsâmolecular fingerprints, descriptors, and graph-based numerical representationsâare rigorously benchmarked. Additionally, a novel training and evaluation data set framework is presented, enabling predictive model training of drug off-target cardiotoxicity using a comprehensive and large curated data set covering these three cardiac ion channels. To facilitate these predictions, a robust and comprehensive small molecule cardiotoxicity prediction tool named CToxPred has been developed. It is made available as open source under the permissive MIT license at https://github.com/issararab/CToxPred.
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Cardiotoxicidad , Canales de Potasio Éter-A-Go-Go , Humanos , Benchmarking , Canales Iónicos , Descubrimiento de Drogas , Bloqueadores de los Canales de Potasio/farmacología , Bloqueadores de los Canales de Potasio/químicaRESUMEN
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus 2019 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications. We have reanalyzed public affinity purification-mass spectrometry data using open modification searching to investigate the presence of post-translational modifications in the context of the SARS-CoV-2 virus-host protein-protein interaction network. Based on an over twofold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. In addition, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.
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COVID-19 , SARS-CoV-2 , Humanos , Interacciones Microbiota-Huesped , Procesamiento Proteico-Postraduccional , Mapas de Interacción de ProteínasRESUMEN
A key analysis task in mass spectrometry proteomics is matching the acquired tandem mass spectra to their originating peptides by sequence database searching or spectral library searching. Machine learning is an increasingly popular postprocessing approach to maximize the number of confident spectrum identifications that can be obtained at a given false discovery rate threshold. Here, we have integrated semisupervised machine learning in the ANN-SoLo tool, an efficient spectral library search engine that is optimized for open modification searching to identify peptides with any type of post-translational modification. We show that machine learning rescoring boosts the number of spectra that can be identified for both standard searching and open searching, and we provide insights into relevant spectrum characteristics harnessed by the machine learning model. The semisupervised machine learning functionality has now been fully integrated into ANN-SoLo, which is available as open source under the permissive Apache 2.0 license on GitHub at https://github.com/bittremieux/ANN-SoLo.
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Péptidos , Programas Informáticos , Bases de Datos de Proteínas , Péptidos/análisis , Espectrometría de Masas en Tándem/métodos , Aprendizaje Automático , Algoritmos , Biblioteca de PéptidosRESUMEN
As current shotgun proteomics experiments can produce gigabytes of mass spectrometry data per hour, processing these massive data volumes has become progressively more challenging. Spectral clustering is an effective approach to speed up downstream data processing by merging highly similar spectra to minimize data redundancy. However, because state-of-the-art spectral clustering tools fail to achieve optimal runtimes, this simply moves the processing bottleneck. In this work, we present a fast spectral clustering tool, HyperSpec, based on hyperdimensional computing (HDC). HDC shows promising clustering capability while only requiring lightweight binary operations with high parallelism that can be optimized using low-level hardware architectures, making it possible to run HyperSpec on graphics processing units to achieve extremely efficient spectral clustering performance. Additionally, HyperSpec includes optimized data preprocessing modules to reduce the spectrum preprocessing time, which is a critical bottleneck during spectral clustering. Based on experiments using various mass spectrometry data sets, HyperSpec produces results with comparable clustering quality as state-of-the-art spectral clustering tools while achieving speedups by orders of magnitude, shortening the clustering runtime of over 21 million spectra from 4 h to only 24 min.
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Algoritmos , Péptidos , Péptidos/análisis , Espectrometría de Masas/métodos , Proteómica/métodos , Análisis por ConglomeradosRESUMEN
spectrum_utils is a Python package for mass spectrometry data processing and visualization. Since its introduction, spectrum_utils has grown into a fundamental software solution that powers various applications in proteomics and metabolomics, ranging from spectrum preprocessing prior to spectrum identification and machine learning applications to spectrum plotting from online data repositories and assisting data analysis tasks for dozens of other projects. Here, we present updates to spectrum_utils, which include new functionality to integrate mass spectrometry community data standards, enhanced mass spectral data processing, and unified mass spectral data visualization in Python. spectrum_utils is freely available as open source at https://github.com/bittremieux/spectrum_utils.
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Proteómica , Programas Informáticos , Espectrometría de Masas , Proteómica/métodos , Metabolómica , Aprendizaje AutomáticoRESUMEN
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.
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Proteoma , Proteómica , Humanos , Estándares de Referencia , Vocabulario Controlado , Espectrometría de Masas , Bases de Datos de ProteínasRESUMEN
The prediction of epitope recognition by T-cell receptors (TCRs) has seen many advancements in recent years, with several methods now available that can predict recognition for a specific set of epitopes. However, the generic case of evaluating all possible TCR-epitope pairs remains challenging, mainly due to the high diversity of the interacting sequences and the limited amount of currently available training data. In this work, we provide an overview of the current state of this unsolved problem. First, we examine appropriate validation strategies to accurately assess the generalization performance of generic TCR-epitope recognition models when applied to both seen and unseen epitopes. In addition, we present a novel feature representation approach, which we call ImRex (interaction map recognition). This approach is based on the pairwise combination of physicochemical properties of the individual amino acids in the CDR3 and epitope sequences, which provides a convolutional neural network with the combined representation of both sequences. Lastly, we highlight various challenges that are specific to TCR-epitope data and that can adversely affect model performance. These include the issue of selecting negative data, the imbalanced epitope distribution of curated TCR-epitope datasets and the potential exchangeability of TCR alpha and beta chains. Our results indicate that while extrapolation to unseen epitopes remains a difficult challenge, ImRex makes this feasible for a subset of epitopes that are not too dissimilar from the training data. We show that appropriate feature engineering methods and rigorous benchmark standards are required to create and validate TCR-epitope predictive models.
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Regiones Determinantes de Complementariedad , Epítopos de Linfocito T , Modelos Genéticos , Modelos Inmunológicos , Receptores de Antígenos de Linfocitos T alfa-beta , Animales , Regiones Determinantes de Complementariedad/genética , Regiones Determinantes de Complementariedad/inmunología , Epítopos de Linfocito T/genética , Epítopos de Linfocito T/inmunología , Humanos , Macaca mulatta , Ratones , Receptores de Antígenos de Linfocitos T alfa-beta/genética , Receptores de Antígenos de Linfocitos T alfa-beta/inmunologíaRESUMEN
Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-cluster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.
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Proteómica , Espectrometría de Masas en Tándem , Algoritmos , Análisis por Conglomerados , Consenso , Bases de Datos de Proteínas , Proteómica/métodos , Programas Informáticos , Espectrometría de Masas en Tándem/métodosRESUMEN
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemically induced, and artifactual modifications. The Human Proteome Organization Proteomics Standards Initiative in collaboration with several members of the Consortium for Top-Down Proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://psidev.info/proforma.
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Proteoma , Proteómica , Humanos , Procesamiento Proteico-Postraduccional , Proteoma/genética , Estándares de Referencia , Programas InformáticosRESUMEN
BACKGROUND: Spectral library searching is currently the most common approach for compound annotation in untargeted metabolomics. Spectral libraries applicable to liquid chromatography mass spectrometry have grown in size over the past decade to include hundreds of thousands to millions of mass spectra and tens of thousands of compounds, forming an essential knowledge base for the interpretation of metabolomics experiments. AIM OF REVIEW: We describe existing spectral library resources, highlight different strategies for compiling spectral libraries, and discuss quality considerations that should be taken into account when interpreting spectral library searching results. Finally, we describe how spectral libraries are empowering the next generation of machine learning tools in computational metabolomics, and discuss several opportunities for using increasingly accessible large spectral libraries. KEY SCIENTIFIC CONCEPTS OF REVIEW: This review focuses on the current state of spectral libraries for untargeted LC-MS/MS based metabolomics. We show how the number of entries in publicly accessible spectral libraries has increased more than 60-fold in the past eight years to aid molecular interpretation and we discuss how the role of spectral libraries in untargeted metabolomics will evolve in the near future.
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Metabolómica , Espectrometría de Masas en Tándem , Metabolómica/métodos , Cromatografía Liquida/métodos , Espectrometría de Masas en Tándem/métodosRESUMEN
The volume of proteomics and mass spectrometry data available in public repositories continues to grow at a rapid pace as more researchers embrace open science practices. Open access to the data behind scientific discoveries has become critical to validate published findings and develop new computational tools. Here, we present ppx, a Python package that provides easy, programmatic access to the data stored in ProteomeXchange repositories, such as PRIDE and MassIVE. The ppx package can be used as either a command line tool or a Python package to retrieve the files and metadata associated with a project when provided its identifier. To demonstrate how ppx enhances reproducible research, we used ppx within a Snakemake workflow to reanalyze a published data set with the open modification search tool ANN-SoLo and compared our reanalysis to the original results. We show that ppx readily integrates into workflows, and our reanalysis produced results consistent with the original analysis. We envision that ppx will be a valuable tool for creating reproducible analyses, providing tool developers easy access to data for development, testing, and benchmarking, and enabling the use of mass spectrometry data in data-intensive analyses. The ppx package is freely available and open source under the MIT license at https://github.com/wfondrie/ppx.
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Proteómica , Programas Informáticos , Espectrometría de Masas , Metadatos , Motor de BúsquedaRESUMEN
The SARS-CoV-2 virus is the causative agent of the 2020 pandemic leading to the COVID-19 respiratory disease. With many scientific and humanitarian efforts ongoing to develop diagnostic tests, vaccines, and treatments for COVID-19, and to prevent the spread of SARS-CoV-2, mass spectrometry research, including proteomics, is playing a role in determining the biology of this viral infection. Proteomics studies are starting to lead to an understanding of the roles of viral and host proteins during SARS-CoV-2 infection, their protein-protein interactions, and post-translational modifications. This is beginning to provide insights into potential therapeutic targets or diagnostic strategies that can be used to reduce the long-term burden of the pandemic. However, the extraordinary situation caused by the global pandemic is also highlighting the need to improve mass spectrometry data and workflow sharing. We therefore describe freely available data and computational resources that can facilitate and assist the mass spectrometry-based analysis of SARS-CoV-2. We exemplify this by reanalyzing a virus-host interactome data set to detect protein-protein interactions and identify host proteins that could potentially be used as targets for drug repurposing.
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COVID-19/virología , Difusión de la Información/métodos , Espectrometría de Masas/métodos , SARS-CoV-2/química , COVID-19/epidemiología , Prueba de COVID-19/métodos , Prueba de COVID-19/estadística & datos numéricos , Biología Computacional , Bases de Datos de Proteínas/estadística & datos numéricos , Reposicionamiento de Medicamentos , Interacciones Microbiota-Huesped/fisiología , Humanos , Espectrometría de Masas/estadística & datos numéricos , Pandemias , Dominios y Motivos de Interacción de Proteínas , Mapas de Interacción de Proteínas , Procesamiento Proteico-Postraduccional , Proteómica/métodos , Proteómica/estadística & datos numéricos , SARS-CoV-2/patogenicidad , SARS-CoV-2/fisiología , Proteínas Virales/química , Proteínas Virales/fisiología , Tratamiento Farmacológico de COVID-19RESUMEN
RATIONALE: Structure elucidation of small molecules has been one of the cornerstone applications of mass spectrometry for decades. Despite the increasing availability of software tools, structure elucidation from tandem mass spectrometry (MS/MS) data remains a challenging task, leaving many spectra unidentified. However, as an increasing number of reference MS/MS spectra are being curated at a repository scale and shared on public servers, there is an exciting opportunity to develop powerful new deep learning (DL) models for automated structure elucidation. ARCHITECTURES: Recent early-stage DL frameworks mostly follow a "two-step approach" that translates MS/MS spectra to database structures after first predicting molecular descriptors. The related architectures could suffer from: (1) computational complexity because of the separate training of descriptor-specific classifiers, (2) the high dimensional nature of mass spectral data and information loss due to data preprocessing, (3) low substructure coverage and class imbalance problem of predefined molecular fingerprints. Inspired by successful DL frameworks employed in drug discovery fields, we have conceptualized and designed hypothetical DL architectures to tackle the above issues. For (1), we recommend multitask learning to achieve better performance with fewer classifiers by grouping structurally related descriptors. For (2) and (3), we introduce feature engineering to extract condensed and higher-order information from spectra and structure data. For instance, encoding spectra with subtrees and pre-calculated spectral patterns add peak interactions to the model input. Encoding structures with graph convolutional networks incorporates connectivity within a molecule. The joint embedding of spectra and structures can enable simultaneous spectral library and molecular database search. CONCLUSIONS: In principle, given enough training data, adapted DL architectures, optimal hyperparameters and computing power, DL frameworks can predict small molecule structures, completely or at least partially, from MS/MS spectra. However, their performance and general applicability should be fairly evaluated against classical machine learning frameworks.