Mass Spectrometry

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Overview

Mass spectrometry measures ions by their mass-to-charge ratios; tandem spectra record molecular fragments that help identify compounds, while imaging and MALDI-TOF support spatial and microbial analyses. Machine-learning approaches include transformer-based spectrum prediction and retrieval, fingerprint prediction, and generative models such as diffusion and flow matching for reconstructing molecular structures or peptide sequences. These methods are tested on benchmarks such as MassSpecGym, NPLIB1, and peptide sequencing datasets, as well as in metabolomics, clinical microbiology, and instrument-transfer settings. A central challenge is that strong benchmark scores may not transfer across instruments, labs, or chemical domains, and data leakage, uncertain predictions, and mismatches between intermediate objectives and real retrieval tasks can undermine reliability.

Latest papers

CardsList

33 papers5 papers in the last four weeks, against 2 the four weeks before. 0.0% of all new papers.

  1. GEMS: Molecular Structure Elucidation as Learned Search over Isomer Graphs

    Oct 16, 2026Utku Umur Acikalin, Yingheng Wang, Goncalo J. Gouveia +3Mass Spectrometry

    Department of Computer Science, Cornell University · Department of Chemistry and Chemical Biology, Cornell University · Boyce Thompson Institute, Cornell University

  2. dIon: Fragmentation-Based Invariance for Self-Supervised Learning of Tandem Mass Spectra

    Oct 5, 2026Alfred Nilsson, Joel Lapin, Samuel H. Payne +2Self-Supervised Pre-TrainingMass Spectrometry

    Science for Life Laboratory, KTH Royal Institute of Technology Stockholm, Sweden · Computational Mass Spectrometry, TUM School of Life Sciences Technical University of Munich, Freising, Germany · Biology Department, Brigham Young University Provo, Utah 84602, United States +1

  3. Explainable Molecular Structure Inference from GC--MS with Diffusion Models and LLM Reranking

    Oct 2, 2026Changlin Liu, Tianyu Yi, Chengchun Liu +2Molecular Graph GenerationMass Spectrometry

  4. Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions

    Sep 30, 2026Ling Min Serena Khook-Nearest NeighborsMass Spectrometry

    MIT

  5. Transferable Mass Spectrum Prediction via Reference-Guided Test-time Specialization

    Sep 28, 2026Yunhua Zhong, Runting Li, Yifan Li +5Test-Time AdaptationContinual Test-Time Adaptation

    The Hong Kong University of Science and Technology (Guangzhou) · The University of Hong Kong · South China University of Technology +3

  6. GyroNovo: Error-Guided Fragment Imputation with Mass-Aware Attention for De Novo Peptide Sequencing

    Sep 24, 2026Abdellah El Mekki, Laks V. S. Lakshmanan, Muhammad Abdul-MageedMass SpectrometryAttention Mechanisms

    The University of British Columbia · Canada Research Chair in NLP and ML

  7. Predicting Collision Cross Sections with GRACE: Geometric Residual Adduct Conditioning via Early-fusion

    Sep 10, 2026Parthasarathy Suryanarayanan, Susanta Das, Shreyans Sethi +2Molecular Property PredictionMass Spectrometry

    IBM Research, Yorktown Heights, NY 10598, United States · Center for Computational Life Sciences, Cleveland Clinic Research, The Cleveland Clinic, Cleveland, OH 44195, United States · Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States

  8. Biologically Informed Representation Learning for Robust Cross-Center Generalization of MALDI-TOF Mass Spectrometry

    Aug 8, 2026Alejandro L. García-Navarro, Carlos Sevilla-Salcedo, Belén Rodríguez-Sánchez +1Domain GeneralizationMass Spectrometry

    Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés, 28911, Spain · Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, 28009 Spain · Clinical Microbiology and Infectious Diseases Department at Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain

  9. MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

    Jul 26, 2026Xin Zhao, Yumin Liu, Zhuo Li +5Language ModelingMolecular Generation

    MoE Key Lab of Artificial Intelligence, AI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai, China · Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China · ByteDance Inc., Beijing, China +1

  10. Agent-Guided Relational Concept Discovery: Toward Interpretable Surgical Margin Assessment

    Jul 23, 2026Nooshin Maghsoodi, Amoon Jamzad, Robert Policelli +11Computational PathologyMass Spectrometry

    Queen’s University, Kingston, ON, Canada

  11. A multiverse-consensus pipeline for reproducible feature selection in untargeted LC-MS metabolomics

    Jul 19, 2026Mohammed Saeed Al-Huraibi, Ihsan Yozgat, Ahmet KaplanFeature SelectionMass Spectrometry

    1Istanbul Medipol University, Istanbul, Turkey · 2Istinye University, Istanbul, Turkey

  12. MARLIN: De Novo Molecular Structure Elucidation from Tandem Mass Spectra without a Ground-Truth Formula

    Jul 6, 2026Xujun Che, Xiuxia Du, Depeng XuMolecular GenerationMass Spectrometry

    Department of Software and Information Systems, University of North Carolina at Charlotte, Charlotte, NC 28223 · Center for Environmental Monitoring and Informatics Technologies for Public Health, University of North Carolina at Charlotte, Charlotte, NC 28223 · Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223

  13. Self-Supervised Calibration of Scientific Instruments Using Physical Consistency Constraints

    Jun 28, 2026M. Rejmund, A. LemassonSelf-Supervised LearningPhysics-Informed ML

    GANIL, CEA/DRF - CNRS/IN2P3, Bd Henri Becquerel, BP 55027, F-14076, Caen Cedex 5, France

  14. GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

    Jun 28, 2026Rui-Xi Wang, Runzhong Wang, Connor W. ColeyMass Spectrometry

    Massachusetts Institute of Technology Cambridge, MA 02139

  15. MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

    Jun 17, 2026Hongxuan Liu, Roman Bushuiev, Ivy Lightheart +12Benchmark DesignBenchmark Contamination

    1Massachusetts Institute of Technology · Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences · 3Czech Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague +2

  16. MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry

    Jun 10, 2026Dongxin Lyu, Jingbo Zhou, Hongxin Xiang +2Memory-Augmented Neural NetworksTransformer Inference

    Westlake University Hangzhou, Zhejiang, China · Hunan University Changsha, Hunan, China · Shanghai Artificial Intelligence Laboratory Shanghai, China +1

  17. The Language of Elution: Autoregressive Prediction of the Next Feature in Untargeted LC-HRMS Lipidomics

    Jun 2, 2026Dayanjan S. WijesingheMass SpectrometrySequence Modeling

    Department of Pharmacotherapy and Outcomes Sciences, Virginia Commonwealth University School of2026 Pharmacy, Richmond, VA 23298, USA

  18. SCENT: Aligning Mass Spectra with Molecular Structure for Olfactory Perception

    May 26, 2026Ziqi Zhang, Eunyeong Jin, Miguel Vasco +6Cross-Modal AlignmentMolecular Property Prediction

    1Dept. of Intelligent Systems, KTH Royal Institute of Technology, Stockholm, Sweden · 2Atmospheric Chemistry Dept., Max Planck Institute for Chemistry, Mainz, Germany · 3Dept. of Information Technology, Uppsala University, Uppsala, Sweden +1

  19. MSAlign: Aligning Molecule and Mass Spectra Foundation Models for Metabolite Identification

    May 19, 2026Paul Krzakala, Gabriel Melo, Camille Lançon +4Distribution ShiftCross-Modal Alignment

    LTCI, Télécom Paris & CMAP, Ecole Polytechnique, Institut Polytechnique de Paris · LTCI, Télécom Paris, Institut Polytechnique de Paris · CEA, INRAE, MetaboHUB, Université Paris-Saclay +1

  20. CoRe-Gen: Robust Spectrum-to-Structure Generation under Imperfect Fingerprint Conditions

    May 13, 2026Tianbo Liu, Chixiang Lu, Jing Hao +4Autoregressive GenerationMolecular Generation

    The University of Hong Kong · The Chinese University of Hong Kong · Zhejiang Shuren University

  21. A Flexible Adaptive Stable Clustering Algorithm for Archive-Scale Online Mass Spectrometry

    May 8, 2026Shao Shi, Xin Yang, Huiran Feng +8Algorithmic StabilityClustering

    Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, 518055, Guangdong, China. · Guangdong Provincial Observation and Research Station for Coastal Atmosphere and Climate of the Greater Bay Area, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, 518055, Guangdong, China.

  22. Unlocking High-Fidelity Molecular Generation from Mass Spectra via Dual-Stream Line Graph Diffusion

    May 7, 2026Xujun Che, Xiuxia Du, Depeng XuGraph Neural NetworksMolecular Graph Generation

    Department of Software and Information Systems,2026 University of North Carolina at Charlotte, Charlotte, NC 28223 · Center for Environmental Monitoring and Informatics Technologies for Public Health University of North Carolina at Charlotte, Charlotte, NC 28223 · Department of Bioinformatics and Genomics,May University of North Carolina at Charlotte, Charlotte, NC 28223

  23. PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

    May 3, 2026Zhiwen Yang, Pan Liu, Yifan Li +2Benchmark DesignBenchmark Contamination

    The Hong Kong University of Science and Technology (Guangzhou). · Yangzhou University. · The Hong Kong University of Science and Technology.

  24. IonMorphNet: Generalizable Learning of Ion Image Morphologies for Peak Picking in Mass Spectrometry Imaging

    Apr 21, 2026Philipp Weigand, Niels Nawrot, Nikolas Ebert +2Representation LearningMass Spectrometry

    Mannheim University of Applied Sciences, Germany · Faculty of Biosciences, Heidelberg University, Germany

  25. FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time

    Apr 17, 2026Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar +4Inference-Time ScalingMolecular Generation

    Massachusetts Institute of Technology, Cambridge, MA, United States · Texas A&M University, College Station, TX, United States

  26. FlowMS: Flow Matching for De Novo Structure Elucidation from Mass Spectra

    Mar 19, 2026Jianan Nie, Peng GaoMass SpectrometryMolecular Graph Generation

    Virginia Tech

  27. When should we trust the annotation? Selective prediction for molecular structure retrieval from mass spectra

    Mar 11, 2026Mira Jürgens, Gaetan De Waele, Morteza Rakhshaninejad +1Selective PredictionMass Spectrometry

    Department of Data Analysis and Mathematical Modeling, Ghent University, Coupure Links 653, Ghent, 9000, Belgium. · Department of Computer Science, University of Antwerp, Middelheimlaan 1, Antwerp, 2020, Belgium.

  28. MS2MetGAN: Latent-space adversarial training for metabolite-spectrum matching in MS/MS database search

    Mar 7, 2026Meng Tsai, Alexzander Dwyer, Estelle Nuckels +1Mass Spectrometry

    Department of Computer Science and Engineering, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, 37403, Tennessee, United States. · Department of Natural Sciences, Middle Georgia State University, 100 University Pkwy, Macon, 31206, Georgia, United States.

  29. FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

    Feb 26, 2026Yunhua Zhong, Yixuan Tang, Yifan Li +5Benchmark DesignMass Spectrometry

    The Hong Kong University of Science and Technology (Guangzhou). · The University of Hong Kong. · Yangzhou University. +3

  30. De novo molecular structure elucidation from mass spectra via flow matching

    Feb 23, 2026Ghaith Mqawass, Tuan Le, Fabian Theis +1Mass SpectrometryMolecular Generation

    TUM School of Life Sciences Weihenstephan, Technical University of Munich, Germany · Machine Learning and Computational Sciences, Pfizer Research & Development, Berlin, Germany · TUM School of Computation, Information and Technology, Technical University of Munich, Germany +1