Kendrick mass calculation

kendrick-mass-calculation

Summary

Calculate Normalized Kendrick Mass (NKM) values from m/z measurements in high-resolution mass spectrometry data to enable visualization and homolog series analysis. NKM transforms m/z data into a standardized coordinate system that reveals hydrocarbon-like homolog patterns in complex mixtures.

When to use

You have uploaded m/z values from a high-resolution mass spectrometry analysis of a complex sample (e.g., crude oil, natural organic matter) and need to visualize homolog series trends. Use this skill when you intend to generate a Kendrick mass plot with a choice between m/z and NKM as the x-axis, or when you need to group or filter peaks by their position in Kendrick space relative to a selected base mass unit (typically CH₂ homologs with base mass 14.0157).

When NOT to use

• Input data lacks an m/z column or does not originate from mass spectrometry analysis
• You need to compare samples using multivariate statistics (use PCA, Matrix, or Venn instead)
• Data are already in formula-space or require network-based homolog relationships (use Network tab)

Inputs

• Delimiter-separated data file (CSV, semicolon, or comma) with column headers
• Column labeled or recognized by keyword 'm/z' containing mass-to-charge ratios
• Column labeled or recognized by keyword 'intensity' containing peak intensities
• Base mass parameter (default: 14.0157 for CH₂; user-editable in parameters tab)

Outputs

• Normalized Kendrick Mass (NKM) vector aligned 1:1 with input m/z values
• Interactive Kendrick mass plot (Canvas A or B) with selectable x-axis (m/z or NKM)
• Tooltip data containing both m/z, NKM, and intensity for each plotted point

How to apply

Extract the m/z column from the uploaded data file using Punc'data's keyword-based column recognition (m/z values are identified automatically). For each m/z value, compute NKM using the formula: NKM = round(m/z × base_mass) − (m/z × base_mass_rounded), where base_mass defaults to 14.0157 for CH₂ homolog series but can be adjusted in the parameters tab for other units of interest. Store both the original m/z and computed NKM vectors alongside their corresponding intensity values. Create a selector control (dropdown or toggle) to allow users to choose whether the x-axis of the Kendrick plot displays 'm/z' or 'NKM'. Pass the user's selected abscissa vector and intensity values to the Canvas renderer to generate the interactive Kendrick mass plot.

Related tools

• Punc'data (Interactive platform for uploading data files, recognizing m/z and intensity columns by keyword, computing NKM values, and rendering the interactive Kendrick mass plot with x-axis selector) — https://github.com/WTVoe/puncdata

Evaluation signals

• NKM values are computed and stored for every input m/z point; output vector length matches input m/z length
• X-axis toggle correctly switches between displaying m/z and NKM without loss of intensity or tooltip data
• NKM values fall within expected range (typically 0–1 in normalized form) and reflect the periodic structure of homolog series
• Interactive plot responds to ctrl+click (pinpoint tooltip), shift+click (zoom), and double-click (reset); points can be selected and deleted
• Base mass parameter in the parameters tab can be edited and plot updates correspondingly

Limitations

• Base mass unit is assumed constant across all m/z values; heterogeneous samples may not fit a single homolog series
• No validation or quality control metrics are documented for m/z accuracy or tolerance
• NKM calculation does not account for instrumental resolution or peak mass accuracy beyond the input precision
• Kendrick plots are visual diagnostic tools; no statistical thresholding or automated homolog assignment is provided

Evidence

• [other] Compute Normalized Kendrick Mass (NKM) values for each peak using the formula NKM = round(m/z × base mass) − (m/z × base mass rounded), where base mass is the mass unit of interest (typically 14.0157 for CH₂ homolog series).: "Compute Normalized Kendrick Mass (NKM) values for each peak using the formula NKM = round(m/z × base mass) − (m/z × base mass rounded), where base mass is the mass unit of interest (typically 14.0157"
• [readme] Punc'data recognizes column information based on keywords such as m/z value, intensity, and formula.: "Punc'data recognizes which column corresponds to which information based on keywords."
• [other] Create a selector control (dropdown or toggle) that stores the user's choice of x-axis coordinate ('m/z' or 'NKM').: "Create a selector control (dropdown or toggle) that stores the user's choice of x-axis coordinate ('m/z' or 'NKM')."
• [other] Implement conditional logic to return the selected abscissa vector: if x-axis mode is 'm/z', return the original m/z column; if 'NKM', return the computed NKM column.: "Implement conditional logic to return the selected abscissa vector: if x-axis mode is 'm/z', return the original m/z column; if 'NKM', return the computed NKM column."
• [readme] Punc'data is an interactive attribution and vizualization tool made for high resolution mass spectrometry results.: "Punc'data is an interactive attribution and vizualization tool made for high resolution mass spectrometry results."