Package: wrTopDownFrag 1.0.2

wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

Top-Down mass spectrometry aims to identify entire proteins as well as their (post-translational) modifications or ions bound (eg Chen et al (2018) <doi:10.1021/acs.analchem.7b04747>). The pattern of internal fragments (Haverland et al (2017) <doi:10.1007/s13361-017-1635-x>) may reveal important information about the original structure of the proteins studied (Skinner et al (2018) <doi:10.1038/nchembio.2515> and Li et al (2018) <doi:10.1038/nchem.2908>). However, the number of possible internal fragments gets huge with longer proteins and subsequent identification of internal fragments remains challenging, in particular since the the accuracy of measurements with current mass spectrometers represents a limiting factor. This package attempts to deal with the complexity of internal fragments and allows identification of terminal and internal fragments from deconvoluted mass-spectrometry data.

Authors:Wolfgang Raffelsberger [aut, cre]

wrTopDownFrag_1.0.2.tar.gz
wrTopDownFrag_1.0.2.zip(r-4.5)wrTopDownFrag_1.0.2.zip(r-4.4)wrTopDownFrag_1.0.2.zip(r-4.3)
wrTopDownFrag_1.0.2.tgz(r-4.5-any)wrTopDownFrag_1.0.2.tgz(r-4.4-any)wrTopDownFrag_1.0.2.tgz(r-4.3-any)
wrTopDownFrag_1.0.2.tar.gz(r-4.5-noble)wrTopDownFrag_1.0.2.tar.gz(r-4.4-noble)
wrTopDownFrag_1.0.2.tgz(r-4.4-emscripten)wrTopDownFrag_1.0.2.tgz(r-4.3-emscripten)
wrTopDownFrag.pdf |wrTopDownFrag.html
wrTopDownFrag/json (API)

# Install 'wrTopDownFrag' in R:
install.packages('wrTopDownFrag', repos = c('https://wraff.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 2 scripts 119 downloads 25 exports 10 dependencies

Last updated 5 years agofrom:d6b00f3a64. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 17 2025
R-4.5-winNOTEMar 17 2025
R-4.5-macNOTEMar 17 2025
R-4.5-linuxNOTEMar 17 2025
R-4.4-winOKMar 17 2025
R-4.4-macOKMar 17 2025
R-4.4-linuxOKMar 17 2025
R-4.3-winOKMar 17 2025
R-4.3-macOKMar 17 2025

Exports:.chargeCatchingAA.checkModTy.countLET.countModif.CtermPepCut.evalIsoFra.exNamesTyDeList.multMatByColNa.NtermPepCut.parCombinateAllAndSum.prefFragPattern.singleSpecModif.termPepCutAAfragSettingsaddMassModifcheckModTycombinateAllAndSumcountChildrenParentcountPotModifAAsevalIsoFragmfragmentSeqidentifFixedModifmakeFragmentsplotNTheorscoreChargeCatch

Dependencies:evaluatehighrknitrlimmaMASSstatmodwrMiscwrProteoxfunyaml

Getting started with wrTopDownFrag

Rendered fromwrTopDownFragVignette1.Rmdusingknitr::rmarkdownon Mar 17 2025.

Last update: 2020-09-08
Started: 2020-09-08