OrgMassSpecR: Organic Mass Spectrometry

Organic/biological mass spectrometry data analysis.

Author
Nathan G. Dodder, with code contributions from Katharine M. Mullen.
Date of publication
2014-05-21 18:02:34
Maintainer
Nathan Dodder <nathand@sccwrp.org>
License
BSD_2_clause + file LICENSE
Version
0.4-4
URLs

View on R-Forge

Man pages

ConvertConcentration
Convert Concentration Basis
ConvertPeptide
Convert peptide sequence.
DeadVolume
Internal volume of tubing.
Digest
Predict Peptides Resulting from Enzymatic Digest
DrawChromatogram
Plot a Chromatogram
example.chromatogram.single
Example Chromatograms
example.sequence
Human Serum Albumin Amino Acid Sequence
example.spectrum.labeled
Example MALDI-TOF Spectrum of Nitrogen-15 Labeled Peptide
example.spectrum.peptide
Example Peptide Fragmentation Spectrum
example.spectrum.unknown
Example EI Fragmentation Spectra
ExchangeableAmides
Determine the Number of Backbone Amide Hydrogens
FlowTime
Solvent transit time.
FragmentPeptide
Predict Peptide Fragment Ions
IsotopicDistribution
Isotopic Distribution of an Organic Molecule.
IsotopicDistributionHDX
Isotopic Distribution of a Peptide Undergoing H-D Exchange
IsotopicDistributionN
Isotopic Distribution of a Nitrogen-15 Labeled Peptide.
ListFormula
Convert an Elemental Formula to a List
MolecularWeight
Calculate the molecular weight of an organic molecule.
MonoisotopicMass
Calculate the monoisotopic mass or monoisotopic m/z value of...
OrgMassSpecR-package
Organic Mass Spectrometry
PeptideSpectrum
Plot Annotated Peptide Fragmentation Mass Spectrum
ReadMspDirectory
Read in MSP Formatted Mass Spectra
ReadMspFile
Read in a MSP Formatted Mass Spectrum
RetentionIndex
Non-Isothermal Retention Index Calculation
SpectrumSimilarity
Similarity Between Two Mass Spectra
WriteMspFile
Write Spectra to the NIST MSP Text Format

Files in this package

OrgMassSpecR/DESCRIPTION
OrgMassSpecR/LICENSE
OrgMassSpecR/NAMESPACE
OrgMassSpecR/R
OrgMassSpecR/R/ConvertConcentration.R
OrgMassSpecR/R/ConvertPeptide.R
OrgMassSpecR/R/DeadVolume.R
OrgMassSpecR/R/Digest.R
OrgMassSpecR/R/DrawChromatogram.R
OrgMassSpecR/R/ExchangeableAmides.R
OrgMassSpecR/R/FlowTime.R
OrgMassSpecR/R/FragmentPeptide.R
OrgMassSpecR/R/IsotopicDistribution.R
OrgMassSpecR/R/IsotopicDistributionHDX.R
OrgMassSpecR/R/IsotopicDistributionN.R
OrgMassSpecR/R/ListFormula.R
OrgMassSpecR/R/MolecularWeight.R
OrgMassSpecR/R/MonoisotopicMass.R
OrgMassSpecR/R/PeptideSpectrum.R
OrgMassSpecR/R/ReadMspDirectory.R
OrgMassSpecR/R/ReadMspFile.R
OrgMassSpecR/R/RetentionIndex.R
OrgMassSpecR/R/SpectrumSimilarity.R
OrgMassSpecR/R/WriteMspFile.R
OrgMassSpecR/build
OrgMassSpecR/build/vignette.rds
OrgMassSpecR/data
OrgMassSpecR/data/example.chromatogram.multiple.txt.gz
OrgMassSpecR/data/example.chromatogram.single.txt.gz
OrgMassSpecR/data/example.sequence.rda
OrgMassSpecR/data/example.spectrum.authentic.txt.gz
OrgMassSpecR/data/example.spectrum.labeled.txt.gz
OrgMassSpecR/data/example.spectrum.peptide.txt.gz
OrgMassSpecR/data/example.spectrum.unknown.txt.gz
OrgMassSpecR/inst
OrgMassSpecR/inst/NEWS.Rd
OrgMassSpecR/inst/doc
OrgMassSpecR/inst/doc/OrgMassSpecR-examples.R
OrgMassSpecR/inst/doc/OrgMassSpecR-examples.Rmd
OrgMassSpecR/inst/doc/OrgMassSpecR-examples.html
OrgMassSpecR/inst/extdata
OrgMassSpecR/inst/extdata/msp
OrgMassSpecR/inst/extdata/msp/pentaBDE.msp
OrgMassSpecR/inst/extdata/msp/unknown.msp
OrgMassSpecR/man
OrgMassSpecR/man/ConvertConcentration.Rd
OrgMassSpecR/man/ConvertPeptide.Rd
OrgMassSpecR/man/DeadVolume.Rd
OrgMassSpecR/man/Digest.Rd
OrgMassSpecR/man/DrawChromatogram.Rd
OrgMassSpecR/man/ExchangeableAmides.Rd
OrgMassSpecR/man/FlowTime.Rd
OrgMassSpecR/man/FragmentPeptide.Rd
OrgMassSpecR/man/IsotopicDistribution.Rd
OrgMassSpecR/man/IsotopicDistributionHDX.Rd
OrgMassSpecR/man/IsotopicDistributionN.Rd
OrgMassSpecR/man/ListFormula.Rd
OrgMassSpecR/man/MolecularWeight.Rd
OrgMassSpecR/man/MonoisotopicMass.Rd
OrgMassSpecR/man/OrgMassSpecR-package.Rd
OrgMassSpecR/man/PeptideSpectrum.Rd
OrgMassSpecR/man/ReadMspDirectory.Rd
OrgMassSpecR/man/ReadMspFile.Rd
OrgMassSpecR/man/RetentionIndex.Rd
OrgMassSpecR/man/SpectrumSimilarity.Rd
OrgMassSpecR/man/WriteMspFile.Rd
OrgMassSpecR/man/example.chromatogram.single.Rd
OrgMassSpecR/man/example.sequence.Rd
OrgMassSpecR/man/example.spectrum.labeled.Rd
OrgMassSpecR/man/example.spectrum.peptide.Rd
OrgMassSpecR/man/example.spectrum.unknown.Rd
OrgMassSpecR/vignettes
OrgMassSpecR/vignettes/OrgMassSpecR-examples.Rmd