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.