9.8 Background removal in MS/MS data

Even if data-dependent acquisition (DDA) is used to acquire MS/MS data, there may still be a substantial number of background peaks present in the MS/MS spectra. The filtering section introduced several filters to remove these.

Another approach to remove background is to identify frequently occurring background peaks, which typically are a sign of contamination in the analytical system, and subsequently remove these. The getBGMSMSPeaks() function inspects all MS/MS data in a set of blank analyses and identifies frequently occurring peaks.

# get background MS/MS peaks from blank analyses
bgPeaks <- getBGMSMSPeaks(anaInfo, replicates = "solvent-pos")

#> Averaging the spectra for each of the 3 analyses
#> Using 'mzr' backend for reading MS data.
#> ================================================================================
#> Averaging analyses averaged spectra... Done!

bgPeaks

#>            mz intensity abundance_rel_ana abundance_abs_ana abundance_rel_spec abundance_abs_spec
#>         <num>     <num>             <num>             <num>              <num>              <num>
#>  1:  98.97532  6325.059                 1                 3          0.4669805           233.3333
#>  2: 100.11211  4400.579                 1                 3          0.2261462           113.0000
#>  3: 101.01768  3430.920                 1                 3          0.2321316           116.0000
#>  4: 102.99709  3728.637                 1                 3          0.3108626           155.3333
#>  5: 107.08547  4883.053                 1                 3          0.5610356           280.3333
#> ---                                                                                              
#> 19: 139.07513  4069.568                 1                 3          0.5043540           252.0000
#> 20: 145.00769 14196.250                 1                 3          0.2955198           147.6667
#> 21: 163.01816 14682.364                 1                 3          0.2988518           149.3333
#> 22: 169.08578  4610.031                 1                 3          0.2307982           115.3333
#> 23: 181.02875  3742.822                 1                 3          0.2401476           120.0000

The replicates function argument tells which analyses are used for blank subtraction, in the above example all the analyses with the replicate set to “solvent-pos” are used. It is also possible to specify multiple replicate names. Typically, you will choose sample analyses here that did not undergo any sample preparation, such as pure solvent blanks.

The filter() function is then used to remove these peaks in the peak list data.

# remove background peaks from MS/MS spectra
mslists <- filter(mslists, removeMZs = bgPeaks)

The removeMZs filter removes all the MS/MS peaks from the mz column. You can also specify a vector with m/z values to remove, for instance, if you identified background peaks by other means than the getBGMSMSPeaks() function.

For more details, see the reference manual (?getBGMSMSPeaks).