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protViz (version 0.1.45)

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Description

This R package helps with quality checks, vizualizations 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

0.1.45

License

GPL-3

Maintainer

Christian Panse

Last Published

April 9th, 2013

Functions in protViz (0.1.45)

massDeviationPlot

Mass Deviation Plot
pgImporter

Progenesis Importer Function
pgLFQaov

iTRAQ two group analysis
parentIonMass

Compute Parent Ion Mass of a Peptide Sequence
pgLFQfeature

pgLFQfeature - A data set with a featuremap export ProgenesisLCMS
pressureProfile

NanoLC pressure profile
pgLFQprot

pgLFQprot - A data set with a featuremap export ProgenesisLCMS
PTM_MarkerFinder

PTM MarkerFinder
pressureProfileSummary

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

LC-MS Map
msms

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

compute a matching between a peptide sequence and a MS2 spectrum
iTRAQ

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

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

Label Free Quantification using the top N peptide approach
de_novo

does de-novo on tandem ms
genMod

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

Compute b and y Fragment Ions of a Peptide Sequence
iTRAQ2GroupAnalysis

iTRAQ two group analysis
PTM_MarkerFinder_util

PTM MarkerFinder util plot
findNN

find index of nearest neighbor
peakplot

Labelling of Peptide Fragment Mass Spectra
swath

SWATH exporter
fetuinLFQ

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

Plotting pressure profile data from Eksigent LC pumps