OrgMassSpecR: Organic Mass Spectrometry

Organic/biological mass spectrometry data analysis.

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
http://OrgMassSpec.github.io/

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.