Bibliospec-class: R access to Bibliospec File
In protViz/bibliospec: Reading and Analyzing Mass Spectrometric Search Results

Description Details Fields Methods Author(s) References See Also Examples

This class implements an R referenz class for BiblioSpec generated sqlite files and can return the data contained as data.frames or as list of tandem mass spectra peptide assignments objects (psm).

The function performs a SQL query on the SQLite files generated by BiblioSpec using the RSQLite package.

BiblioSpec files are generated by using Skyline or the BiblioSpec command line tool available from protwiz.

.data: private
dbfile: database file location
peaksTable: name of peaks table. do not modify

annotatePeaksWithFragments(error = 10, ppm = TRUE, neutralloss = c(Citrulline_Ornithine = -43.005814), excludeAA = "B|X|Z"): annotate database table, be carefull might run for a while
getAnnotedPeaks(): Get peak lists with Ion annotation.
getModification(): modification table
getNrPSM(): Get number of psm's in database.
getPeaks(): Get peaks - mz and intensity and spectra id as data.frame.
getPeaksAsList(): preparing Peaks as a list, will take a while if you blib file is large.
getPeaksSummaries(): Get summaries for all peaks. Might be huge!
getPeaksWithMeta(): Get peaks with all the meta information as data.frame. Might be huge!
getPsmSet(): get class psmSet S3 (list of psm objects). psm objects can be viewed by using the peakplot method of package protViz.
getSpectraMeta(): Get spectra meta information - retention time , file name, num peaks as data.frame
listTables(): List tables in db
summary(): summary of bibliospec file

Witold E. Wolski and Christian Panse

UNIT 13.7 Using BiblioSpec for Creating and Searching Tandem MS, Peptide Libraries. Barbara Frewen, Michael J. MacCoss. Current Protocols in Bioinformatics Current Protocols in Bioinformatics. http://dx.doi.org/10.1002/0471250953.bi1307s20.
The predecessor of the method getPsmSet was implemented in the bioconductor package specL:

Panse C, Trachsel C, Grossmann J and Schlapbach R. (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics. http://dx.doi.org/10.1093/bioinformatics/btv105.

library(bibliospec)

# use the sqlite file provided in the package
dbfile <- file.path(path.package("bibliospec"),
 "extdata/peptideStd.sqlite")

# call constructor
BS <- Bibliospec(dbfile=dbfile)
stopifnot(BS$getNrPSM() == 137)
S <- BS$getPsmSet()

## Not run: 
 library(specL)
 print(S)
 lapply(S[1:10], plot)

## End(Not run)

peaks <- BS$getPeaks()

print(BS$summary())
head(peaks)

colnames(peaks)

spectrMet <- BS$getSpectraMeta()

# have a look at RT algiment
dim(spectrMet)
data("iRTpeptides")
head(iRTpeptides)
colnames(spectrMet)
x <- merge(spectrMet, iRTpeptides , by.x="peptideSeq", by.y="peptide" )
plot(x$iRT, x$retentionTime)

alldata <- BS$getPeaksWithMeta()
alldata <- merge(spectrMet, peaks)
colnames(BS$getSpectraMeta())
head(BS$getPeaksSummaries()) 

tmp <-merge(BS$getSpectraMeta(),BS$getPeaksSummaries(), by="RefSpectraId" )
head(tmp)