Annotate a Peaktable
Functions which annotate a peaktable on the bases af a database of standards. Not meant to be called directly by the user.
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A vector with three elements in the form
A peaktable (matrix) with three column corresponding to mz,rt and I values for a series of features.
The file containing the error function used to predict the
tolerance on the
A dataframe used for the annotation. See the help of
The subset of settings contained into the "match2DB" element of the XCMSsettings list.
The annotation of each feature is performed by comparing its m/z value and its retention time to a database provided by the user. To account for shifts in retention time and mass occurring during data acquisition, the matching of a specific feature against the DB is done with a specific tolerance in mass and in retention time.
Retention time tolerance
The retention time tolerance is specified (in minutes) in the settings list (field
rttol). This value is instrument- and
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
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 (
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
A list with the following elements
The names of the annotated compounds
The IDs of the annotated compounds
The features with multiple annotations
The features with annotation
N. Shahaf, P. Franceschi, P. Arapitsas, I. Rogachev, U. Vrhovsek and R. Wehrens: "Constructing a mass measurement error surface to improve automatic annotations in liquid chromatography/mass spectrometry based metabolomics". Rapid Communications in Mass Spectrometry, 27(21), 2425 (2013).
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