findMsMsHR.ticms2 {RMassBank} | R Documentation

## Extract an MS/MS spectrum from MS2 TIC

### Description

Extract an MS/MS spectrum or multiple MS/MS spectra based on the TIC of the MS2 and precursor mass, picking the most intense MS2 scan. Can be used, for example, to get a suitable MS2 from direct infusion data which was collected with purely targeted MS2 without MS1.

### Usage

    findMsMsHR.ticms2(
      msRaw,
      mz,
      limit.coarse,
      limit.fine,
      rtLimits = NA,
      maxCount = NA,
      headerCache = NULL,
      fillPrecursorScan = FALSE,
      deprofile = getOption("RMassBank")$deprofile,
      trace = "ms2tic"
    )

### Arguments

`msRaw` | The mzR raw file
`mz` | Mass to find
`limit.coarse` | Allowed mass deviation for scan precursor (in m/z values)
`limit.fine` | Unused here, but present for interface compatiblity with findMsMsHR
`rtLimits` | Unused here, but present for interface compatiblity with findMsMsHR
`maxCount` | Maximal number of spectra to return
`headerCache` | Cached results of header(msRaw), either to speed up the operations or to operate with preselected header() data
`fillPrecursorScan` | Unused here, but present for interface compatiblity with findMsMsHR
`deprofile` | Whether deprofiling should take place, and what method should be used (cf. `deprofile`)
`trace` | Either `"ms2tic"` or `"ms2basepeak"`: Which intensity trace to use - can be either the TIC of the MS2 or the basepeak intensity of the MS2.

### Details

Note that this is not a precise function and only really makes sense in direct infusion and if the precursor is really known, because MS2 precursor data is only "roughly" accurate (to 2 dp). The regular `findMsMsHR` functions confirm the exact mass of the precursor in the MS1 scan.

### Value

a list of "spectrum sets" as defined in `findMsMsHR`, sorted by decreasing precursor intensity.

### Author(s)

stravsmi

[Package RMassBank version 3.0.0 Index]