read.tdf - Bruker timsTOF reader

[cpanse]

read.tdf <- function(filename){
  con <- dbConnect(RSQLite::SQLite(), filename)
  rv <- dbGetQuery(con, "SELECT * FROM Precursors a INNER JOIN Frames b on a.id == b.id;");
  dbDisconnect(con)

  rv <- rv[, c('Id','Time','ScanNumber','Intensity','SummedIntensities',
               'MonoisotopicMz', 'Charge', 'MsMsType')];
  colnames(rv) <- c('scanNumber','StartTime','BasePeakMass','BasePeakIntensity',
                    'totIonCurrent', 'PrecursorMass','ChargeState','MSOrder')
  rv$filename <- basename(filename)
  rv$MSOrder[rv$MSOrder == 0] <- "Ms"
  rv$MSOrder[rv$MSOrder == 8] <- "Ms2"
  as.rawDiag(rv)
}

[cpanse]

check 'MsMsType' 8 and 0