OrgMassSpecR: Organic Mass Spectrometry
Version 0.4-4

Organic/biological mass spectrometry data analysis.

Browse man pages Browse package API and functions Browse package files

AuthorNathan G. Dodder, with code contributions from Katharine M. Mullen.
Date of publication2014-05-21 18:02:34
MaintainerNathan Dodder <nathand@sccwrp.org>
LicenseBSD_2_clause + file LICENSE
Version0.4-4
URL http://OrgMassSpec.github.io/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("OrgMassSpecR", repos="http://R-Forge.R-project.org")

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

Functions

ConvertConcentration Man page Source code
ConvertPeptide Man page Source code
DeadVolume Man page Source code
Digest Man page Source code
DrawChromatogram Man page Source code
ExchangeableAmides Man page Source code
FlowTime Man page Source code
FragmentPeptide Man page Source code
IsotopicDistribution Man page Source code
IsotopicDistributionHDX Man page Source code
IsotopicDistributionN Man page Source code
ListFormula Man page Source code
MolecularWeight Man page Source code
MonoisotopicMass Man page Source code
OrgMassSpecR Man page
OrgMassSpecR-package Man page
PeptideSpectrum Man page Source code
ReadMspDirectory Man page Source code
ReadMspFile Man page Source code
RetentionIndex Man page Source code
SpectrumSimilarity Man page Source code
WriteMspFile Man page Source code
example.chromatogram.multiple Man page
example.chromatogram.single Man page
example.sequence Man page
example.spectrum.authentic Man page
example.spectrum.labeled Man page
example.spectrum.peptide Man page
example.spectrum.unknown Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/ConvertConcentration.R
R/ConvertPeptide.R
R/DeadVolume.R
R/Digest.R
R/DrawChromatogram.R
R/ExchangeableAmides.R
R/FlowTime.R
R/FragmentPeptide.R
R/IsotopicDistribution.R
R/IsotopicDistributionHDX.R
R/IsotopicDistributionN.R
R/ListFormula.R
R/MolecularWeight.R
R/MonoisotopicMass.R
R/PeptideSpectrum.R
R/ReadMspDirectory.R
R/ReadMspFile.R
R/RetentionIndex.R
R/SpectrumSimilarity.R
R/WriteMspFile.R
build
build/vignette.rds
data
data/example.chromatogram.multiple.txt.gz
data/example.chromatogram.single.txt.gz
data/example.sequence.rda
data/example.spectrum.authentic.txt.gz
data/example.spectrum.labeled.txt.gz
data/example.spectrum.peptide.txt.gz
data/example.spectrum.unknown.txt.gz
inst
inst/NEWS.Rd
inst/doc
inst/doc/OrgMassSpecR-examples.R
inst/doc/OrgMassSpecR-examples.Rmd
inst/doc/OrgMassSpecR-examples.html
inst/extdata
inst/extdata/msp
inst/extdata/msp/pentaBDE.msp
inst/extdata/msp/unknown.msp
man
man/ConvertConcentration.Rd
man/ConvertPeptide.Rd
man/DeadVolume.Rd
man/Digest.Rd
man/DrawChromatogram.Rd
man/ExchangeableAmides.Rd
man/FlowTime.Rd
man/FragmentPeptide.Rd
man/IsotopicDistribution.Rd
man/IsotopicDistributionHDX.Rd
man/IsotopicDistributionN.Rd
man/ListFormula.Rd
man/MolecularWeight.Rd
man/MonoisotopicMass.Rd
man/OrgMassSpecR-package.Rd
man/PeptideSpectrum.Rd
man/ReadMspDirectory.Rd
man/ReadMspFile.Rd
man/RetentionIndex.Rd
man/SpectrumSimilarity.Rd
man/WriteMspFile.Rd
man/example.chromatogram.single.Rd
man/example.sequence.Rd
man/example.spectrum.labeled.Rd
man/example.spectrum.peptide.Rd
man/example.spectrum.unknown.Rd
vignettes
vignettes/OrgMassSpecR-examples.Rmd
OrgMassSpecR documentation built on May 21, 2017, 4:04 a.m.