Package: nontarget 2.2

Martin Loos

nontarget: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data

Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.

Authors:Martin Loos

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nontarget.pdf |nontarget.html✨
nontarget/json (API)
NEWS

# Install 'nontarget' in R:

install.packages('nontarget', repos = c('https://rickhelmus.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/blosloos/nontarget/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

peaklist - HRMS peak list

On CRAN:

2.33 score 3 stars 18 scripts 73 downloads 2 mentions 18 exports 115 dependencies

Last updated 2 years agofrom:e302215851. Checks:OK: 1 NOTE: 8. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 12 2024
R-4.5-win-x86_64	NOTE	Oct 13 2024
R-4.5-linux-x86_64	NOTE	Oct 13 2024
R-4.4-win-x86_64	NOTE	Nov 12 2024
R-4.4-mac-x86_64	NOTE	Nov 12 2024
R-4.4-mac-aarch64	NOTE	Sep 13 2024
R-4.3-win-x86_64	NOTE	Nov 12 2024
R-4.3-mac-x86_64	NOTE	Nov 12 2024
R-4.3-mac-aarch64	NOTE	Sep 13 2024

Exports:adduct.search combine deter.iso homol.search make.isos ms.filter pattern.search pattern.search2 plotadduct plotall plotcomp plotdefect plotdiff plotgroup plothomol plothomolplotly plotisotopes rm.sat

Dependencies:askpass backports base64enc bit bit64 blob broom bslib cachem callr cellranger cli clipr colorspace conflicted cpp11 crayon crosstalk curl data.table DBI dbplyr digest dplyr dtplyr enviPat evaluate fansi farver fastmap fontawesome forcats fs gargle generics ggplot2 glue googledrive googlesheets4 gtable haven highr hms htmltools htmlwidgets httr ids isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lubridate magrittr MASS Matrix memoise mgcv mime modelr munsell nlme nontargetData openssl pillar pkgconfig plotly prettyunits processx progress promises ps purrr R6 ragg rappdirs RColorBrewer Rcpp readr readxl rematch rematch2 reprex rlang rmarkdown rstudioapi rvest sass scales selectr stringi stringr sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom withr xfun xml2 yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Detecting Isotope, Adduct and Homologue Relations in LC-MS Data.	nontarget-package nontarget
Detecting and grouping adduct m/z relations among peaks in a HRMS dataset	adduct.search
Combining isotope, adduct and homologue series relations in HRMS data sets.	combine
Generating list of type iso from filtered m/z differences.	deter.iso
Homologue series extraction from LC-MS data.	homol.search
Deriving list of m/z isotope differences for input into 'pattern.search'.	make.isos
Flexible interactive filtering of components and/or peaks via polygon selection.	ms.filter
Detecting and grouping isotope m/z relations among peaks in a HRMS dataset	pattern.search
Detecting and grouping isotope m/z relations among LC-HRMS centroid peaks, based on quantized reference data	pattern.search2
HRMS peak list	peaklist
Plot of frequencies and peak intensities of different adducts	plotadduct
RT vs. m/z scatterplot marking isotope pattern and adduct group peaks.	plotall
Plot and print isotope and adduct relations among peaks of a single component	plotcomp
Mass defect vs. m/z scatterplot of HRMS peaks, with specific m/z isotope differences highlighted.	plotdefect
Filtering important m/z differences among peaks of a HRMS data set.	plotdiff
Barplot of m/z isotope (and optional adduct) relations within an isotope pattern group.	plotgroup
Marks homologue series peaks in a scatterplot of retention time (RT) vs. m/z	plothomol
Creates interactive visualization from the output of homol.search() of retention time (RT) vs. m/z	plothomolplotly
Plot of isotope counts over isotope pattern groups or components.	plotisotopes
Removal of satellite peaks from FT-MS peak lists	rm.sat