Chromatographic profile quality assessment

chromatographic-profile-quality-assessment

Summary

Identify and diagnose artefacts (e.g. sawtooth profiles) in extracted ion chromatograms (EICs) produced by peak-detection workflows on LC-MS data with complex scan-window configurations. This skill detects when improper mass-range separation causes filtering of empty spectra within the processing pipeline, degrading peak profile quality.

When to use

Apply this skill when running targeted peak detection on LC-MS data acquired with multiple overlapping m/z scan windows and observing distorted or periodically discontinuous peak profiles in EIC plots. The sawtooth artefact surfaces specifically when tardisPeaks() processes data without proper mass_range argument routing to segregate scan windows by mass range.

When NOT to use

• Input data is acquired with single, non-overlapping m/z scan windows—sawtooth artefacts do not occur in this simpler configuration.
• EIC output already displays clean, continuous peak profiles—the skill is redundant if the artefact is absent.
• Raw data has not been centroided or is in non-mzML format—the skill requires preprocessed, standardized input.

Inputs

• centroided mzML files (LC-MS raw data)
• Spectra objects (loaded from mzML)
• target list data.frame (columns: compound ID, name, m/z, RT, polarity)

Outputs

• EIC plots (Extracted Ion Chromatogram visualizations)
• visual comparison of peak profiles (with/without artefacts)
• diagnostic assessment of mass_range parameter configuration

How to apply

Execute tardisPeaks() twice: first with multi-window mass_range configuration without scan-window separation enabled, then re-execute with corrected mass_range argument routing that segregates scan windows by mass range. Load centroided mzML files as Spectra objects and define a target list data.frame with compound ID, name, m/z, RT, and polarity columns. Generate and visually inspect EIC plots from both runs side-by-side: the first should exhibit sawtooth profiles (jagged, discontinuous intensity baseline) while the second should display clean, continuous peak profiles. The artefact arises because improper mass_range configuration causes TARDIS to filter empty spectra within individual scan windows, creating gaps in the EIC that render as sawtooth discontinuities. Correct mass_range separation ensures all spectra are retained and properly integrated across overlapping windows.

Related tools

• TARDIS (performs targeted peak detection and EIC generation; exposes mass_range parameter controlling scan-window segregation) — https://github.com/pablovgd/TARDIS
• Spectra (loads and represents centroided MS data in memory; integrates with TARDIS workflow)
• xcms (provides retention-time correction algorithm underlying TARDIS processing)
• ProteoWizard/MSConvert (converts proprietary MS file formats to centroided mzML for input to TARDIS)

Examples

library(TARDIS); targets <- data.frame(cmpd_id=c('A','B'), name=c('CompA','CompB'), mz=c(200.05,250.10), rt=c(5.2,8.1), polarity=c('positive','positive')); result_bad <- tardisPeaks(file_path='data.mzML', targets=targets, mass_range=c(150,350)); result_good <- tardisPeaks(file_path='data.mzML', targets=targets, mass_range=list(c(150,250),c(200,350)));

Evaluation signals

• Visual inspection of EIC plots: incorrect mass_range configuration produces sawtooth (jagged, periodic discontinuities in baseline intensity); correct configuration yields smooth, continuous peak profiles.
• Consistency of peak profile shape across replicate runs with identical correct mass_range configuration—repeated runs should produce visually identical EICs.
• Presence/absence of empty spectra filtering artifacts: log or debug output from tardisPeaks() should indicate no empty-spectra filtering when mass_range segregation is properly configured.
• Peak integration metrics (AUC, max intensity, SNR) should be stable and reproducible when mass_range is corrected; unstable metrics with sawtooth profiles suggest uncontrolled artefact.
• Comparison of EIC appearance before and after mass_range correction: the same compound should show visibly discontinuous intensity baseline before correction and smooth baseline after.

Limitations

• The sawtooth artefact is specific to multi-window m/z acquisition schemes; single-window data will not exhibit this failure mode.
• Visual inspection of EIC plots is the primary diagnostic method—no automated detection algorithm is documented in the article, so assessment is subjective and operator-dependent.
• The skill assumes the user can correctly specify the mass_range parameter; no automated validation or suggestion mechanism is mentioned in the README or article.
• EIC quality depends on upstream data preprocessing (centroiding, format conversion); corrupted or poorly centroided mzML files may exhibit spurious artefacts unrelated to mass_range configuration.

Evidence

• [full_text] sawtooth_artefact_definition: "Peaks display a sawtooth profile when tardisPeaks() processes data with multiple overlapping m/z scan windows without mass_range separation, due to filtering of empty spectra within TARDIS."
• [intro] eic_workflow_step: "Execute tardisPeaks() with multi-window mass_range configuration without scan-window separation enabled, generating EIC plots that exhibit sawtooth artefacts."
• [full_text] correction_method: "Re-execute tardisPeaks() with correct mass_range argument routing to segregate scan windows by mass range, producing clean chromatographic peak profiles."
• [intro] target_list_specification: "Define a target list data.frame with compound ID, name, m/z, RT, and polarity columns."
• [full_text] eic_output_inspection: "Save both sets of EIC plots and inspect for artefact presence/absence as visual confirmation of scan-window routing impact."
• [intro] centroided_input_requirement: "Input files need to be converted to the .mzML format and have to be centroided"
• [intro] polarity_filtering_automatic: "Polarity filtering is done within TARDIS, so no polarity subsetting has to be performed"