Retention time intensity tabulation

retention-time-intensity-tabulation

Summary

Extract and tabulate retention time paired with summed intensity values for a target mass-to-charge ratio across all scans in a resolved mzML/mzXML spectrum file. This skill produces a two-column chromatographic profile (retention_time, intensity) suitable for visualization and downstream analysis of LC-MS data.

When to use

When you have a resolved mzML or mzXML spectrum file and need to visualize or analyze the temporal intensity profile of a specific analyte (defined by its m/z value). Apply this skill when you want to reconstruct an extracted-ion chromatogram (XIC) by filtering MS1 scans within a specified mass tolerance window and recovering the chromatographic shape.

When NOT to use

• Input spectrum file is already a feature table, intensity matrix, or pre-computed chromatogram; skip to visualization or statistical analysis.
• MS level is not MS1 or the spectrum file contains only MS2/MS3 fragmentation data without parent-scan retention times.
• Target m/z value is unknown or ambiguous; use feature detection or mass calibration workflows first to identify analyte m/z values.

Inputs

• mzML or mzXML spectrum file (resolved, centroided or profile)
• target m/z value (xicmz, e.g. 870.954)
• mass tolerance (xic_tolerance, e.g. 0.5 Th or ppm)
• normalization flag (xic_norm, boolean or string)

Outputs

• two-column tabular data file (retention_time, intensity)
• extracted-ion chromatogram (XIC) profile
• intensity-versus-retention-time paired values

How to apply

Load the mzML or mzXML file using a mass spectrometry parser (e.g., pyteomics or mzmine). Filter all MS1 scans to extract signals within the specified m/z tolerance window (e.g., xicmz ± tolerance in ppm or Th, such as 870.954 ± 0.5). For each scan, record the retention time and sum all intensities across the filtered m/z range. Tabulate the retention time and summed intensity as paired values and export as a two-column data file. Apply normalization if requested (e.g., xic_norm parameter) to scale intensity values relative to the chromatogram's maximum.

Related tools

• GNPS LCMS Visualization Dashboard (Primary tool for accepting resolved mzML/mzXML files and parameters (xicmz, xic_tolerance, xic_norm) and computing and displaying the extracted-ion chromatogram.) — https://github.com/Wang-Bioinformatics-Lab/GNPS_LCMSDashboard
• pyteomics (Mass spectrometry data parser library for reading and filtering mzML/mzXML files at the programmatic level.)
• mzmine (Standalone mass spectrometry data processing tool for filtering MS1 scans and extracting ion chromatograms.)

Examples

https://gnps-lcms.ucsd.edu/?usi=mzspec%3AMSV000084951%3AAH22&xicmz=870.9543493652343&xic_tolerance=0.5&xic_norm=False&show_ms2_markers=True&ms2_identifier=None

Evaluation signals

• Output file contains exactly two columns with numeric retention time and intensity values, with no missing or malformed entries.
• All output retention times are within the observed range of the input spectrum file (e.g., 0–60 minutes).
• Summed intensity values in the output match hand-calculated sums of all signals within the specified m/z tolerance window for spot-check scans.
• When normalized, maximum intensity in the output equals 1.0 or 100 (depending on normalization scheme); unnormalized values reflect raw detector counts.
• XIC peak shape is smooth and unimodal or multimodal as expected for the analyte; sharp discontinuities or singleton spikes indicate parsing or filtering errors.

Limitations

• Accuracy depends on correct specification of xic_tolerance; too-wide tolerance windows will co-extract isobaric or near-isobaric species, inflating intensity.
• MS1-only filtering excludes MS2/MS3 scans; if retention time metadata is absent or inconsistent, tabulation may fail or produce gaps.
• Normalization is applied globally to the entire chromatogram; if baseline drift or instrument noise is significant, normalized intensity may misrepresent true analyte abundance.
• Does not account for detector saturation, ion suppression, or chromatographic tailing; raw tabulated values reflect these artifacts.

Evidence

• [other] The dashboard accepts resolved mzML/mzXML spectrum files and parameters including xicmz (target m/z value, e.g. 870.954), xic_tolerance (mass tolerance window, e.g. 0.5), and xic_norm (normalization option), then computes the extracted-ion chromatogram by filtering and integrating spectral intensities within the specified mass range across all retention times.: "The dashboard accepts resolved mzML/mzXML spectrum files and parameters including xicmz (target m/z value, e.g. 870.954), xic_tolerance (mass tolerance window, e.g. 0.5), and xic_norm (normalization"
• [other] Load the mzML or mzXML file using a mass spectrometry data parser (e.g., pyteomics or mzmine). Filter all MS1 scans to extract signals within the specified m/z tolerance window (e.g., xicmz ± tolerance in ppm or Th). For each scan, record the retention time and summed intensity across the filtered m/z range. Tabulate retention time and intensity as paired values and export as a two-column data file (retention_time, intensity).: "For each scan, record the retention time and summed intensity across the filtered m/z range. Tabulate retention time and intensity as paired values and export as a two-column data file"
• [other] Filter all MS1 scans to extract signals within the specified m/z tolerance window (e.g., xicmz ± tolerance in ppm or Th).: "Filter all MS1 scans to extract signals within the specified m/z tolerance window (e.g., xicmz ± tolerance in ppm or Th)."
• [readme] To get everything up and running, we've created a make target for you to get docker up and running: make server-compose-interactive. The requirements on your local system are: 1. Docker 2. Docker Compose. This will bring the server up on http://localhost:6548.: "This will bring the server up on http://localhost:6548."