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mascotparser's Introduction

mascotParser

A parser for Mascot search results ( both PMF and MSMS) in R package.

How to install "mascotParser"

From Github using R:

install.packages("devtools")
library("devtools")
install_github("mascotParser","nghiavtr")
library("mascotParser")

##1. Example for parsing MSMS Mascot search result files:

library(MascotParser)
filename <- "MSMS_Mascot_search_result.dat";

#####parse the dat file

myParse <- parse(new("MascotParser"),filename)
Get MS1 peaks
myParse@qexp
myParse@qintensity
how many query of MS2 in this data set?
myParse@MSMSnumQuery
how many hits and hit scores from these query?
myParse@PIHnumHits
myParse@PIHhitScores
Extract information of MS2 peaks from query 3
myms2=getMSMSqueryInfo(myParse,3)
myms2$mz
myms2$intensity
plot MS1 mass spetrum
plotSpec(myParse,specTitle=NULL,queryId=NULL)
plot mass spectrum of query 1
plotSpec(myParse,specTitle=NULL,queryId=1)
draw a panel plot of MS2 peaks from query 1 and query 2
mz1=getMSMSqueryInfo(myParse,1)$mz
int1=getMSMSqueryInfo(myParse,1)$intensity
mz2=getMSMSqueryInfo(myParse,2)$mz
int2=getMSMSqueryInfo(myParse,2)$intensity
plotSpecPanel(mz1,int1,mz2,int2,xlimVal=500,plotTitle="test title")

##2. Example for parsing PMF Mascot search result files:

library(MascotParser)
filename <- "PMF_Mascot_search_result.dat";
parse the dat file
myParse <- parse(new("MascotParser"),filename)
get unassigned peaks from the search
negPeaks <- myParse@qexp[getUnassignedPeaks(myParse, scoreThres=MascotThres)]
plot PMF mass spetrum
plotSpec(myParse,specTitle=NULL,queryId=NULL)

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