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Comparative Evaluations of Mass Spectral Data Bases

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In silico MS/MS prediction for peptidoglycan profiling uncovers novel anti-inflammatory peptidoglycan fragments of the gut microbiota

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Computer-Assisted Structure Identification (CASI)—An Automated Platform for High-Throughput Identification of Small Molecules by Two-Dimensional Gas Chromatography Coupled to Mass Spectrometry

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Benefit of the Use of GCxGC/MS Profiles for 1D GC/MS Data Treatment Illustrated by the Analysis of Pyrolysis Products from East Asian Handmade Papers

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Various aspects of retention index usage for GC-MS library search: A statistical investigation using a diverse data set

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Improving the Screening Analysis of Pesticide Metabolites in Human Biomonitoring by Combining High-Throughput In Vitro Incubation and Automated LC–HRMS Data Processing

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Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules

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Mass spectrometry fingerprinting coupled to National Institute of Standards and Technology Mass Spectral search algorithm for pattern recognition

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Rapid oligonucleotide drug impurity determination by direct spectral comparison of ion‐pair reversed‐phase high‐performance liquid chromatography electrospray ionization mass spectrometry data

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A comparative study for the organic byproducts from hydrothermal carbonizations of sugarcane bagasse and its bio-refined components cellulose and lignin

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Constructing a data-driven receptor model for organic and inorganic aerosol – a synthesis analysis of eight mass spectrometric data sets from a boreal forest site

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Deep learning-based method for automatic resolution of gas chromatography-mass spectrometry data from complex samples

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Differentiation of the Stereochemistry and Anomeric Configuration for 1-3 Linked Disaccharides Via Tandem Mass Spectrometry and 18O-labeling

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Method for the elucidation of the elemental composition of low molecular mass chemicals using exact masses of product ions and neutral losses: application to environmental chemicals measured by liquid chromatography with hybrid quadrupole/time‐of‐flight mass spectrometry

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Universal bacterial identification by mass spectrometry of 16S ribosomal RNA cleavage products

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Insights into mutualism mechanism and versatile metabolism of Ketogulonicigenium vulgare Hbe602 based on comparative genomics and metabolomics studies

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Statistical comparison of mass spectra for identification of amphetamine-type stimulants

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Analysis of the Association between Fatigue and the Plasma Lipidomic Profile of Inflammatory Bowel Disease Patients

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Machine learning model for detecting fentanyl analogs from mass spectra

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A large scale test dataset to determine optimal retention index threshold based on three mass spectral similarity measures

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Establishment of a knowledge base for identification of residual solvents in pharmaceuticals

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COSS: A Fast and User-Friendly Tool for Spectral Library Searching

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Vital Carbohydrate and Lipid Metabolites in Serum Involved in Energy Metabolism during Pubertal Molt of Mud Crab (Scylla paramamosain)

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Updates to the Inverted Library Search Algorithm for Mixture Analysis

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Identifying xenobiotic metabolites with in silico prediction tools and LCMS suspect screening analysis

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Empowering the rapid authentication of the botanical origin of monofloral honey by coated blade spray mass spectrometry (CBS-MS)

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Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries

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AMDIS in the Chemical Weapons Convention

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Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Typings of Edible Oils through Spectral Networking of Triacylglycerol Fingerprints

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Pattern Similarity Measures Applied to Mass Spectra

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Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams

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Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences

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Digging deeper - A new data mining workflow for improved processing and interpretation of high resolution GC-Q-TOF MS data in archaeological research

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Recent Developments Toward Integrated Metabolomics Technologies (UHPLC-MS-SPE-NMR and MicroED) for Higher-Throughput Confident Metabolite Identifications

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Application of Comprehensive 2D Gas Chromatography Coupled with Mass Spectrometry in Beer and Wine VOC Analysis

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Statistical approach to establish equivalence of unabbreviated mass spectra

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Methods to Calculate Spectrum Similarity

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Evaluation of hop (Humulus lupulus) as a repellent for the management of Drosophila suzukii

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Data Processing, Metabolomic Databases and Pathway Analysis

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Open, High-Resolution EI+ Spectral Library of Anthropogenic Compounds

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Minimum variance optimized Fisher ratio analysis of comprehensive two-dimensional gas chromatography / mass spectrometry data: Study of the pacu fish metabolome

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Fragmentation Energy Index for Universalization of Fragmentation Energy in Ion Trap Mass Spectrometers for the Analysis of Chemical Weapon Convention Related Chemicals by Atmospheric Pressure Ionization-Tandem Mass Spectrometry Analysis

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Prediction of Peptide Fragment Ion Mass Spectra by Data Mining Techniques

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Optimizing targeted/untargeted metabolomics by automating gas chromatography/mass spectrometry workflows

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Effect of storage on microbioa and enzyme proteomic profile of low-temperature Daqu

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Unsupervised neural networks as a support tool for pathology diagnosis in MALDI-MSI experiments: A case study on thyroid biopsies

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ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization

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Improving Accuracy and Confidence of Chemical Identification by Gas Chromatography/Vacuum Ultraviolet Spectroscopy-Mass Spectrometry: Parallel Gas Chromatography, Vacuum Ultraviolet, and Mass Spectrometry Library Searches

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Spectral Library Searching for Peptide Identification via Tandem MS

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Bicyclobutonium ion versus cyclopropylcarbinyl cation chemistry: the cycloaddition reaction with ethene in the dilute gas phase

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CMSSP: A Contrastive Mass Spectra-Structure Pretraining Model for Metabolite Identification

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Simulating comprehensive two-dimensional gas chromatography mass spectrometry data with realistic run-to-run shifting to evaluate the robustness of tile-based Fisher ratio analysis

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On-chip Raman spectrometers using narrow band filter array combined with CMOS image sensors

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BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring

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Mass spectra prediction with structural motif-based graph neural networks

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Seasonal Differences in Submicron Marine Aerosol Particle Organic Composition in the North Atlantic

Lewis, S. L., Saliba, G., Russell, L. M., Quinn, P. K., Bates, T. S., & Behrenfeld, M. J. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.720208 · Cited by 19

A Review on GC-MS and Method Development and Validation

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New Library-Based Methods for Nontargeted Compound Identification by GC-EI-MS

McGlynn, D., Yee, L. D., Garraffo, H. M., Geer, L. Y., Mak, T. D., Mirokhin, Y. A., Tchekhovskoi, D. V., Jen, C. N., Goldstein, A. H., Kearsley, A. J., et al. (2025) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00451 · Cited by 18

Metabolomic changes in Caenorhabditis elegans lifespan mutants as evident from GC–EI–MS and GC–APCI–TOF–MS profiling

Jaeger, C., Tellström, V., Zurek, G., König, S., Eimer, S., & Kammerer, B. (2014) · Metabolomics · doi:10.1007/s11306-014-0637-y · Cited by 18

Data Programs at NBS/NIST: 1901–2021

SEMERJIAN, H. G., & Burgess, D. R. (2022) · Journal of Physical and Chemical Reference Data · doi:10.1063/5.0084230 · Cited by 18

Evaluation of Ion Mobility Spectrometry for Improving Constitutional Assignment in Natural Product Mixtures

Neto, F. C., Clark, T. N., Lopes, N. P., & Linington, R. G. (2022) · Journal of Natural Products · doi:10.1021/acs.jnatprod.1c01048 · Cited by 18

Sensitive and reliable multianalyte quantitation of herbal medicine in rat plasma using dynamic triggered multiple reaction monitoring

Yan, Z., Li, T., Lv, P., Li, X., Zhou, C., & Yang, X. (2013) · Journal of Chromatography B · doi:10.1016/j.jchromb.2013.03.019 · Cited by 18

Protein Turnover Quantification in a Multilabeling Approach: From Data Calculation to Evaluation

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BiPACE 2D—graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry

Hoffmann, N., Wilhelm, M., Doebbe, A., Niehaus, K., & Stoye, J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt738 · Cited by 18

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2)

de Oliveira, G. S., Kawahara, R., Rosa-Fernandes, L., Mule, S. N., Avila, C. C., Teixeira, M. M. G., Larsen, M. R., & Palmisano, G. (2018) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0006351 · Cited by 18

Revisiting Five Years of CASMI Contests with EPA Identification Tools

McEachran, A. D., Chao, A., Al-Ghoul, H., Lowe, C. N., Grulke, C., Sobus, J. R., & Williams, A. J. (2020) · Metabolites · doi:10.3390/metabo10060260 · Cited by 18

A general approach to study molecular fragmentation and energy redistribution after an ionizing event

Erdmann, E., Aguirre, N. F., Indrajith, S., Chiarinelli, J., Domaracka, A., Rousseau, P., Huber, B., Bolognesi, P., Richter, R., Avaldi, L., et al. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp04890a · Cited by 18

CsoDIAq Software for Direct Infusion Shotgun Proteome Analysis

Cranney, C., & Meyer, J. G. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c02021 · Cited by 18

Revealing Unknown Controlled Substances and New Psychoactive Substances Using High-Resolution LC–MS-MS Machine Learning Models and the Hybrid Similarity Search Algorithm

Lee, S. Y., Lee, S. T., Suh, S., Ko, B. J., & Oh, H. B. (2021) · Journal of Analytical Toxicology · doi:10.1093/jat/bkab098 · Cited by 20

Resolving isobaric interferences in direct infusion tandem mass spectrometry

Kaeslin, J., & Zenobi, R. (2022) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.9266 · Cited by 17

Prediction of electron ionization mass spectra based on graph convolutional networks

Zhang, B., Zhang, J., Xia, Y., Chen, P., & Wang, B. (2022) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2022.116817 · Cited by 20

Machine learning-assisted non-target analysis of a highly complex mixture of possible toxic unsymmetrical dimethylhydrazine transformation products with chromatography-mass spectrometry

Sholokhova, A. Y., Grinevich, O. I., Matyushin, D. D., & Buryak, A. K. (2022) · Chemosphere · doi:10.1016/j.chemosphere.2022.135764 · Cited by 18

Scribe: Next Generation Library Searching for DDA Experiments

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Calculation of retention time tolerance windows with absolute confidence from shared liquid chromatographic retention data

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Electron Ionization Mass Spectrometry for Both Liquid and Gas Chromatography in One System without the Need for Hardware Adjustments

Tsizin, S., Fialkov, A. B., & Amirav, A. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00136 · Cited by 18

Optimization and evaluation of spectral comparisons of electrical tape backings by X-ray fluorescence

Brooks, E. J., Mehltretter, A. H., Prusinowski, M. N., & Trejos, T. (2020) · Forensic Chemistry · doi:10.1016/j.forc.2020.100291 · Cited by 17

CRB-SWATH: A Method for Enhancing Untargeted Precursor Ion Extraction and Automatically Constructing Their Tandem Mass Spectra from SWATH Datasets by Chromatographic Retention Behaviors

Wang, R., Ding, J., Geng, Y., Li, Y.-Z., Mei, Y., Bao, K., Yu, H.-D., & Feng, Y. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c01841 · Cited by 17

An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification

Houthuijs, K. J., Berden, G., Engelke, U. F. H., Gautam, V., Wishart, D. S., Wevers, R. A., Martens, J. K., & Oomens, J. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01078 · Cited by 17

De Novo Cleaning of Chimeric MS/MS Spectra for LC-MS/MS-Based Metabolomics

Zhao, T., Xing, S., Yu, H., & Huan, T. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c00736 · Cited by 17

Machine learning‐based peptide‐spectrum match rescoring opens up the immunopeptidome

Adams, C., Laukens, K., Bittremieux, W., & Boonen, K. (2023) · PROTEOMICS · doi:10.1002/pmic.202300336 · Cited by 16

ChloroDBPFinder: Machine Learning-Guided Recognition of Chlorinated Disinfection Byproducts from Nontargeted LC-HRMS Analysis

Zhao, T., Wawryk, N. J. P., Xing, S., Low, B., Li, G., Yu, H., Wang, Y., Shen, Q., Li, X., & Huan, T. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c05124 · Cited by 20

Sex-dependent changes in the skin mucus metabolome of discus fish (Symphysodon haraldi) during biparental care

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Preliminary effects of real-world factors on the recovery and exploitation of forensic impurity profiles of a nerve-agent simulant from office media

Fraga, C. G., Sego, L. H., Hoggard, J. C., Acosta, G. A. P., Viglino, E., Wahl, J. H., & Synovec, R. E. (2012) · Journal of Chromatography A · doi:10.1016/j.chroma.2012.10.053 · Cited by 17

Gas Chromatography-Tandem Mass Spectrometry of Lignin Pyrolyzates with Dopant-Assisted Atmospheric Pressure Chemical Ionization and Molecular Structure Search with CSI:FingerID

Larson, E. A., Hutchinson, C. P., & Lee, Y. (2018) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-018-2001-3 · Cited by 17

Protein Analysis by Shotgun Proteomics

Gao, Y., & Yates, J. R. (2019) · Wiley eBooks · doi:10.1002/9781118970195.ch1 · Cited by 21

Unveiling the dark matter of the metabolome: A narrative review of bioinformatics tools for LC-HRMS-based compound annotation

Xu, R., & Zhu, J. (2025) · Talanta · doi:10.1016/j.talanta.2025.128327 · Cited by 17

Detecting the sources of chemicals in the Black Sea using non-target screening and deep learning convolutional neural networks

Alygizakis, ‪., Γιαννακόπουλος, Θ., Τhomaidis, Ν. S., & Slobodnı́k, J. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.157554 · Cited by 17

Applying graph neural network models to molecular property prediction using high-quality experimental data

Qu, C., Schneider, B. I., Kearsley, A. J., Keyrouz, W., & Allison, T. C. (2024) · Artificial Intelligence Chemistry · doi:10.1016/j.aichem.2024.100050 · Cited by 17

Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium

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Follicular Fluid Metabolite Changes in Dairy Cows with Inactive Ovary Identified Using Untargeted Metabolomics

Bai, Y., Zhang, F., Zhang, H., Xu, C., Wu, L., & Xia, C. (2020) · BioMed Research International · doi:10.1155/2020/9837543 · Cited by 16

Selection of neutral losses and characteristic ions for mass spectral classifier

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Billionfold data increase from mass spectrometry instrumentation

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Characterization of Sea Surface Microlayer and Marine Aerosol Organic Composition Using STXM-NEXAFS Microscopy and FTIR Spectroscopy

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Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics

McGann, C. D., Barshop, W. D., Canterbury, J. D., Lin, C., Gabriel, W., Huang, J., Bergen, D., Zabrouskov, V., Melani, R. D., Wilhelm, M., et al. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00085 · Cited by 16

Structural annotation of unknown molecules in a miniaturized mass spectrometer based on a transformer enabled fragment tree method

Yang, Y., Sun, S., Yang, S., Yang, Q., Lu, X., Wang, X., Yu, Q., Huo, X., & Qian, X. (2024) · Communications Chemistry · doi:10.1038/s42004-024-01189-0 · Cited by 15

Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics

Lee, J., Tantillo, D. J., Wang, L., & Fiehn, O. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00760 · Cited by 15

Isotope Cluster-Based Compound Matching in Gas Chromatography/Mass Spectrometry for Non-Targeted Metabolomics

Wegner, A., Sapcariu, S. C., Weindl, D., & Hiller, K. (2013) · Analytical Chemistry · doi:10.1021/ac303774z · Cited by 15

Database Searching for Structural Identification of Metabolites in Complex Biofluids for Mass Spectrometry-Based Metabonomics

Kertesz, T. M., Hill, D. W., Albaugh, D., Hall, L. H., Hall, L. M., & Grant, D. F. (2009) · Bioanalysis · doi:10.4155/bio.09.145 · Cited by 15

Evaluation of mass spectral library search algorithms implemented in commercial software

Samokhin, A. S., Sotnezova, K. M., Lashin, V. V., & Revelsky, I. A. (2015) · Journal of Mass Spectrometry · doi:10.1002/jms.3591 · Cited by 61

New algorithm for the identification of mass spectra by the computer library search

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A matching algorithm for library searching of mass spectrum

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Two-step spectral library pre-search: A novel approach for speeding up compound identification

Zhu, Q., Yu, J., Hu, J., & Ding, C. (2017) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2017.03.007 · Cited by 5

Library Search of Mass Spectra with a New Matching Algorithm Based on Substructure Similarity

Gan, F., Yang, J., & Liang, Y. (2001) · Analytical Sciences · doi:10.2116/analsci.17.635 · Cited by 15