findMsMsHR.ticms2 {RMassBank} | R Documentation |
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.
findMsMsHR.ticms2(msRaw, mz, limit.coarse, limit.fine, rtLimits = NA, maxCount = NA, headerCache = NULL, fillPrecursorScan = FALSE, deprofile = getOption("RMassBank")$deprofile, trace = "ms2tic")
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. |
trace |
Either |
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.
a list of "spectrum sets" as defined in findMsMsHR
, sorted
by decreasing precursor intensity.
stravsmi