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:
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-4.4-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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:d6b00f3a64. Checks:OK: 5 NOTE: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 17 2024 |
R-4.5-win | NOTE | Nov 17 2024 |
R-4.5-linux | NOTE | Nov 17 2024 |
R-4.4-win | OK | Nov 17 2024 |
R-4.4-mac | OK | Nov 17 2024 |
R-4.3-win | OK | Nov 17 2024 |
R-4.3-mac | OK | Nov 17 2024 |
Exports:.chargeCatchingAA.checkModTy.countLET.countModif.CtermPepCut.evalIsoFra.exNamesTyDeList.multMatByColNa.NtermPepCut.parCombinateAllAndSum.prefFragPattern.singleSpecModif.termPepCutAAfragSettingsaddMassModifcheckModTycombinateAllAndSumcountChildrenParentcountPotModifAAsevalIsoFragmfragmentSeqidentifFixedModifmakeFragmentsplotNTheorscoreChargeCatch
Dependencies:evaluatehighrknitrlimmaMASSstatmodwrMiscwrProteoxfunyaml
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Settings for AA fragments | AAfragSettings |
Add modifications to peptide mass | addMassModif |
Check & complete mixed of variable and fixed modifications | checkModTy |
Full combinatorial and cumulative values | combinateAllAndSum |
Identify Children/Parent settings as a+b=c | countChildrenParent |
Make table with counts of potential modification sites | countPotModifAAs |
Evaluate selected lines of pepTab (iso-mass) for preferential cutting sites | evalIsoFragm |
Fragment protein or peptide sequence | fragmentSeq |
Identify Fixed Modifications | identifFixedModif |
Make terminal and internal fragments from proteins | makeFragments |
Plot the number of theoretical random fragments | plotNTheor |
Scoring of charge catching potential for peptides | scoreChargeCatch |