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protViz (version 0.1.76)

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Description

This R package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do solid data analysis for small scale data sets.

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Version

Install

install.packages('protViz')

Monthly Downloads

444

Version

0.1.76

License

GPL-3

Maintainer

Christian Panse

Last Published

November 11th, 2013

Functions in protViz (0.1.76)

HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques

Compute b and y Fragment Ions of a Peptide Sequence

averagine - a data set conatining isotope envelopes of averagine peptides

pgLFQfeature - A data set with a featuremap export ProgenesisLCMS

find isotop pattern in a given mass spectrum

find index of nearest neighbor

Progenesis Importer Function

swath library generator

PTM_MarkerFinder_util

PTM MarkerFinder util plot

pressureProfilePlot

Plotting pressure profile data from Eksigent LC pumps

de-novo on tandem ms

massDeviationPlot

Mass Deviation Plot

iTRAQ2GroupAnalysis

iTRAQ two group analysis

compute a matching between a peptide sequence and a MS2 spectrum

A data set containing tandem mass spectra of an LCMS experiment.

pressureProfile

NanoLC pressure profile

pgLFQprot - A data set with a featuremap export ProgenesisLCMS

pressureProfileSummary

A misc function for finding NN time slots in pressure profile data.

PTM_MarkerFinder

PTM MarkerFinder

Compute Parent Ion Mass of a Peptide Sequence

fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.

AA - amino acid table

Label Free Quantification using the top N peptide approach

Labelling of Peptide Fragment Mass Spectra

iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.

iRT peptides - independent retention time peptides

iTRAQ two group analysis

Generates all possible modification of a given peptide seqence and modification pattern

find index of nearest neighbor