Mission and Editorial Ethos

Mass spectrometry (MS) is now foundational to modern molecular science. The technology enables precise measurement of mass‑to‑charge ratios, fragmentation pathways, and molecular structures across small molecules, complex biomolecules, and materials. JDMS exists to accelerate credible progress in MS by publishing work that improves instrument performance, acquisition strategies, sample preparation, separation methods, ionization, fragmentation, informatics, and end‑to‑end workflows. We emphasize methodological clarity, rigorous validation, transparent reporting, and practical reproducibility so that published research can be directly reused, extended, and trusted by the community.

Our editorial stance is explicitly author‑respectful and reader‑centric. Submissions are evaluated by subject‑matter experts who understand current MS practice—bench‑level constraints, data analysis pipelines, standard reference materials, and regulatory expectations. We aim for decisions that are both fast and fair, with detailed feedback focused on scientific soundness, real‑world impact, and clarity of communication. As an open access journal, we ensure immediate global visibility and long‑term accessibility via persistent DOIs and archiving.

Scope and Topical Coverage

JDMS welcomes original research, comprehensive reviews, technical notes, tutorials, perspective articles, benchmark datasets, and software papers across the MS spectrum. We particularly encourage submissions that demonstrate improvements over existing methods through quantitative metrics (e.g., limits of detection/quantitation, dynamic range, mass accuracy, resolving power, throughput, matrix tolerance), rigorous controls, and clearly documented protocols. Representative scope pillars include, but are not limited to:

Author‑Focused Reporting Standards

To help readers assess credibility and reuse results, JDMS expects submissions to provide sufficient methodological detail and validation. Wherever applicable, authors should report calibration materials, sample preparation protocols (e.g., extraction, cleanup, solid‑phase extraction), chromatographic conditions (columns, gradients, flow rates), ionization settings, acquisition parameters, and post‑processing steps. For quantitative methods, please include linearity, LOD/LOQ, precision/accuracy, carryover, recovery, and robustness analysis.

Article Types

• Original Research: Full studies demonstrating methodological or application‑level advances with quantitative evaluation.
• Technical Notes: Focused improvements (hardware, methods, algorithms) with clear benchmarks.
• Reviews & Tutorials: Authoritative syntheses, best‑practice guides, and instructional resources for practitioners.
• Software & Data Resources: Tools, libraries, pipelines, and datasets with documented performance and licensing.
• Perspectives & Commentaries: Expert viewpoints on emerging techniques, standards, and community practices.

Peer Review, Ethics, and Editorial Policies

JDMS operates a rigorous peer‑review process guided by subject‑area editors and supported by qualified reviewers. We follow established publishing ethics and best practices to safeguard research integrity, conflict‑of‑interest disclosure, and transparency. Detailed policies are available on the journal website.

Preparing and Submitting Your Manuscript

Authors should prepare manuscripts according to our formatting guidance and ensure that methods and parameters are reported with sufficient precision to enable reproduction. Where possible, include instrument model/firmware, chromatographic consumables, spectral library details, software versions, search parameters, and calibration curves. Use appropriate controls and reference materials; provide justifications for any deviations from recognized standards in your subfield.

Quality Assurance, Validation, and Reporting Checklists

Across application areas (e.g., metabolomics, clinical toxicology, biotherapeutic characterization), the robustness of an MS workflow depends on appropriate standards, controls, and validation. JDMS encourages authors to provide checklists or tables summarizing key metrics and acceptance criteria so that reviewers and readers can quickly assess method fitness for purpose. Typical elements include system suitability, calibration model, linearity range, carryover, recovery, matrix effects, stability, intra/inter‑day precision, and re‑injection reproducibility. For label‑free proteomics, report peptide and protein FDR thresholds, minimum unique peptides, normalization strategies, and imputation policies, where applicable.

Advanced Topics and Emerging Directions

The MS field is rapidly evolving. JDMS actively covers emerging techniques and interdisciplinary opportunities, with an eye toward practical adoption. Areas of special interest include:

• DIA Workflows: Library‑based and library‑free DIA, ion mobility‑enhanced DIA, and algorithms for deconvolving chimeric spectra.
• Top‑Down Proteomics: Intact protein analysis, native MS, fragmentation strategies for large/heterogeneous proteoforms, and PTM localization.
• Imaging MS: Spatially resolved molecular mapping in tissues and materials; co‑registration, normalization, and hyperspectral analytics.
• Ambient Ionization: Rapid, in situ analyses (DESI, DART, paper spray) for field‑deployable or bedside applications.
• Quantitative Omics: Isotope‑based and label‑free quantitation, batch effect correction, internal standardization, and cross‑lab harmonization.
• MS‑Enabled Structural Biology: Crosslinking MS, hydrogen–deuterium exchange (HDX), ion mobility‑derived collision cross sections, and integrative modeling.
• AI/ML for MS: Deep learning for spectrum annotation, de‑novo sequencing, noise suppression, peak picking, and multimodal integration.

Indexing, Visibility, and Discoverability

As an open access journal, JDMS maximizes the discoverability of your research through metadata quality, persistent identifiers, and search‑friendly presentation. Articles are prepared with clear titles, structured abstracts, informative keywords, and accessible language to help both expert and interdisciplinary audiences. We encourage authors to provide graphical summaries where appropriate and to adopt community taxonomies (e.g., controlled vocabularies for techniques and targets) for better search recall.

Community, Reuse, and Citation Practices

We believe that method papers and datasets are most valuable when they are extensible. JDMS welcomes submissions that not only publish results but also lower barriers for reuse: permissive code licenses, containerized analysis, test datasets with documentation, and step‑wise protocols that can be reproduced in other labs. When reporting comparative performance, please describe baselines, configurations, and statistical tests. Cite prior art fairly and link to repositories/registries so that readers can build upon your contribution.

Getting Started and Staying Informed

New to JDMS? Explore our current and archived content for exemplars in your area of interest. Review instructions for authors before drafting your manuscript. If you have questions about scope fit or methodological expectations, contact the editorial office at [email protected].

Why Publish with JDMS