Metabolomics analysis services: LC-MS and GC-MS workflows from raw spectra to annotated features

Martín-Blázquez et al. (2019): untargeted LC-HRMS on 65 metastatic CRC and 60 control sera identified altered sphingolipids, glycerophospholipids, and an endocannabinoid.

Salihovic et al. [15]: UPLC-MS in 1,424 Swedish adults linked lower 3-hydroxyundecanoyl-carnitine to prevalent T2D; six metabolites improved incident prediction (C-statistic 0.866 to 0.892).

Lloyd-Price et al. [16]: 132 longitudinal IBD subjects with integrated metabolomics, metagenomics, and host transcriptomics linked metabolic shifts to disease activity.

Roth & Powers [17]: 24 PDAC studies; 10 metabolites validated across cohorts, but 87% of 655 proposed biomarkers appeared in only one study.

Clark et al. [18]: proteogenomic profiling of 103 tumors and 80 normal tissues showed oxidative phosphorylation dysregulation at the protein level not apparent from RNA-seq, which is a reason to add matched metabolomics when sample IDs align.

MS1-only matches carry higher false-discovery risk than MS/MS-confirmed identifications [2]. Pepkio assigns annotation tiers and reports putative versus confirmed counts in the QC summary.

Only about 8% of features overlapped across four workflows (XCMS, MS-DIAL, MZmine, Compound Discoverer) on a shared LC-MS dataset [19]. Pepkio locks pipeline and parameters at kickoff.

Batch-associated missingness (BEAMs) can bias imputation and batch correction if handled sequentially [1, 9]. Pepkio profiles missingness by batch and applies batch adjustment only when batch is not confounded with condition.

Signal intensity can shift across injection order and matrix complexity [1, 2]. Pepkio uses pooled QC samples where feasible and applies QC-RLSC or PQN with run-order diagnostics.

Meta-analysis of 24 PDAC studies found that 87% of proposed biomarkers appeared in single reports only [7]. Pepkio recommends validation cohorts before biomarker claims.

Provide raw MS files (`.raw`, `.wiff`, `.d`, or mzML), metadata with condition and batch columns, and platform plus polarity mode. Include pooled QC files when available [1, 2]. Pre-processed peak tables from MS-DIAL or MZmine are accepted when export parameters are documented.

Standard untargeted LC-MS projects (roughly 10-40 samples, one contrast) typically complete in 2-4 weeks. GC-MS extensions, multi-omics integration, multi-contrast designs, or large batch-correction studies may take 4-8 weeks. Exact timelines are confirmed at kickoff.

You receive feature and annotation tables, differential-abundance results per contrast, PCA/PLS-DA and volcano figures (PDF/SVG), an HTML QC report, commented R scripts with conda or `renv` lock files, a README, and a Methods draft. Optional GitHub or Zenodo archival is available on request.

Thermo `.raw`, Agilent `.d`, Bruker `.d`, and Waters `.raw` are converted to mzML via msconvert or imported in MS-DIAL when scoped. SCIEX `.wiff` can be processed in MS-DIAL 5.1 when that workflow is scoped at kickoff, and mzML exports are also accepted. The Methods draft records preprocessing tool, m/z tolerance, and RT alignment parameters.

Pepkio documents TIC quality, missing-value fractions, and outlier samples in the QC report before differential testing. High missingness triggers a review of imputation strategy, including small-value, k-nearest neighbours, or complete-case analysis [1, 9]. Re-analysis after sample re-measurement is discussed when QC threatens the study question.

You retain full ownership of all code and results. Pepkio delivers commented R scripts with conda or `renv` lock files listing exact package versions, organized by pipeline stage with a README.

Checkpoint reviews occur after raw-data QC, after normalization and batch diagnostics, and before final delivery. You can review contrast definitions, normalization, imputation, and annotation thresholds within agreed scope. A dedicated scientific contact leads the project.

Post-delivery support covers clarification of methods, QC thresholds, and minor figure or table revisions within agreed scope (typically ≤20% of deliverables). Substantial new analyses are scoped as separate milestones, consistent with Pepkio's reviewer-support policy.

Metabolomics can be integrated with RNA-seq or proteomics when sample IDs match across layers. Pepkio scopes multi-omics integration via MOFA2 for unsupervised factor discovery or mixOmics DIABLO when a supervised outcome label exists [12, 13]. Cross-layer correlation and pathway concordance are documented in the Methods draft.

Bespoke analyses, including custom contrasts, cross-cohort harmonization, lipid class-specific workflows, network propagation, ML classifiers, or non-standard deliverables, are scoped at kickoff after a feasibility review.