OrgMassSpecR: Organic Mass Spectrometry

Organic/biological mass spectrometry data analysis.

Install the latest version of this package by entering the following in R:
install.packages("OrgMassSpecR")
AuthorNathan Dodder [cre, aut, cph], Katharine Mullen [ctb]
Date of publication2016-10-19 13:07:09
MaintainerNathan Dodder <ndodder@mail.sdsu.edu>
LicenseBSD_2_clause + file LICENSE
Version0.4-6
http://OrgMassSpec.github.io/

View on CRAN

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
ConvertPeptide Man page
DeadVolume Man page
Digest Man page
DrawChromatogram Man page
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
ExchangeableAmides Man page
FlowTime Man page
FragmentPeptide Man page
IsotopicDistribution Man page
IsotopicDistributionHDX Man page
IsotopicDistributionN Man page
ListFormula Man page
MolecularWeight Man page
MonoisotopicMass Man page
OrgMassSpecR Man page
OrgMassSpecR-package Man page
PeptideSpectrum Man page
ReadMspDirectory Man page
ReadMspFile Man page
RetentionIndex Man page
SpectrumSimilarity Man page
WriteMspFile Man page

Files

inst
inst/NEWS.Rd
inst/extdata
inst/extdata/msp
inst/extdata/msp/unknown.msp
inst/extdata/msp/pentaBDE.msp
inst/doc
inst/doc/OrgMassSpecR-examples.Rmd
inst/doc/OrgMassSpecR-examples.html
inst/doc/OrgMassSpecR-examples.R
NAMESPACE
data
data/example.spectrum.peptide.txt.gz
data/example.spectrum.labeled.txt.gz
data/example.chromatogram.single.txt.gz
data/example.spectrum.authentic.txt.gz
data/example.spectrum.unknown.txt.gz
data/example.chromatogram.multiple.txt.gz
data/example.sequence.rda
R
R/DeadVolume.R R/PeptideSpectrum.R R/IsotopicDistribution.R R/ListFormula.R R/SpectrumSimilarity.R R/MonoisotopicMass.R R/ReadMspFile.R R/DrawChromatogram.R R/ConvertPeptide.R R/FlowTime.R R/MolecularWeight.R R/IsotopicDistributionN.R R/WriteMspFile.R R/Digest.R R/IsotopicDistributionHDX.R R/RetentionIndex.R R/FragmentPeptide.R R/ExchangeableAmides.R R/ConvertConcentration.R R/ReadMspDirectory.R
vignettes
vignettes/OrgMassSpecR-examples.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/IsotopicDistribution.Rd man/ExchangeableAmides.Rd man/example.spectrum.unknown.Rd man/IsotopicDistributionHDX.Rd man/ConvertPeptide.Rd man/DrawChromatogram.Rd man/example.spectrum.peptide.Rd man/MonoisotopicMass.Rd man/example.chromatogram.single.Rd man/RetentionIndex.Rd man/MolecularWeight.Rd man/WriteMspFile.Rd man/FlowTime.Rd man/example.sequence.Rd man/ConvertConcentration.Rd man/ListFormula.Rd man/FragmentPeptide.Rd man/example.spectrum.labeled.Rd man/ReadMspFile.Rd man/PeptideSpectrum.Rd man/OrgMassSpecR-package.Rd man/Digest.Rd man/IsotopicDistributionN.Rd man/DeadVolume.Rd man/SpectrumSimilarity.Rd man/ReadMspDirectory.Rd
LICENSE

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

Please suggest features or report bugs with the GitHub issue tracker.

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