## Annotate one feature
AnnotateFeature(input, DB, settings, errf)
## Annotate a full table of features
AnnotateTable(peaktable, errf, DB, settings)(mz,rt,I).m/z value used for the matching against the
DB.LCDBtest for a description of the DB.data.frame withe the results of the
annotation and the reference to the DBrttol). This value is instrument- and
chromatography-dependent.
m/z tolerance
The tolerance on the mass scale mainly depends on the characteristics
of the spectrometer used for the acquisition. For Q-TOF instruments it
has been recently shown (see references) that the optimal mass
tolerance can be expressed as a function of the m/z value and
of the logarithm of the ion intensity log10(I). As a trend, the
mass drift will be bigger for smaller ions and for low intensity
signals.
In the present implementation the tolerance in mass can be either
fixed over the complete mass range or calculated as a function of the
mz and I values of each feature. In the simplest case, the fixed mass
tolerance is provided in the mzwindow (in Dalton!) element of
the list of settings.
Alternatively, one can provide (supplying the errf argument) a
function used to calculate the mz tolerance (in ppm!) as a function of
the fields of the input vector ((mz,rt,I)).
As discussed in the publication, for a Waters Synapt Q-TOF the
function is a linear model taking as inputs M = input["mz"],
logI = log10(input["I"]). This error function can be calculated by
analyzing the results of the injections of the chemical standards. To
avoid unreasonable small errors where data for mz and I are not
available, the minimum value for the mass tolerance is explicitly set
in the settings (ppm). This value should match the technical
characteristics of the spectrometer.
To reduce the number of false positives and make the annotation more
reliable, a match is retained only if more than one feature
associated to a specific compound is found in the list of
features. How many "validation" features are required is defined in the
list of settings in the minfeat element. At this validation
level, another retention time tolerance is introduced:
two or more features validate one specific annotation if their retention
time are not very much different. This rt tolerance is also defined in
the settings (the rtval field). As a general suggestion,
rtval should be kept smaller than rttol. The latter,
indeed, refers to the matching of a peaktable with a database which
has been created from the injections of the chemical standards during
different instrumental runs (maybe also with different columns). On
the other hand, rtval accounts for smaller retention time
shifts, occurring within the same LC run. For the description of the structure of the DB, refer to the help of the
LCDBtest dataset.