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commonMZ

R-CMD-check pkgdown Lifecycle: experimental GitHub release License: MIT Last commit GitHub issues

A curated collection of common m/z values, mass differences, and annotation rules for mass spectrometry, distributed as an R package.

Documentation: stanstrup.github.io/commonMZ

Contributions are welcomed.

Articles

Article What it covers
Looking up a mass difference Search a measured peak-to-peak delta against every catalogued adduct, fragment, and repeating-unit difference
Using commonMZ rules with CAMERA Build CAMERA annotation rule tables and annotate an LC-MS dataset end-to-end
Isotope fine structure Simulate and resolve the individual isotopologues hidden inside an M+1 or M+2 peak
Looking up an isotopologue offset Identify which element a satellite peak a few mDa from M+1/M+2 comes from

Installation

# Bioconductor dependency
if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("CAMERA")

# commonMZ from GitHub
if (!require("remotes")) install.packages("remotes")
remotes::install_github("stanstrup/commonMZ")

Raw data files

The underlying tables are plain-text TSV files in inst/ and colour-coded Excel files, usable independently of R:

  • adducts_fragments.tsv: adduct and neutral-loss mass differences
  • repeating_units_+.tsv / repeating_units_-.tsv: homologous-series steps in positive and negative mode
  • contaminants_+.tsv / contaminants_-.tsv: common background ions
  • CAMERA_rules_pos.xlsx, CAMERA_rules_neg.xlsx, CAMERA_rules_EI.xlsx: CAMERA annotation rule tables

References

The data in these tables are primarily from Keller BO, Sui J, Young AB, Whittal RM. Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta. 2008;627(1):71–81. Per-entry source references are listed in the mass difference lookup article.