msPurity
Bioc currentAutomated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
165 19 exported
Complexity
4.8 avg / 34 max
Call network
165 nodes / 119 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
21,466
Files
160
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
140
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.20
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
13
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 39 (1 internal)includes a package overview page
- Examples that run
- 97%32 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/computational-metabolomics/mspurity on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
Topics
Suggested by (1)
People
- Thomas N. Lawson author maintainer
- Warwick Dunn thesis advisor
- Ossama Edbali contributor
- Andris Jankevics contributor
- Martin Jones contributor
- Julien Saint-Vanne contributor
- Mark Viant thesis advisor
- Ralf Weber contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("msPurity")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1021/acs.analchem.6b04358.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.