R/13_metIdentify_mass_dataset.R
metIdentify_mass_dataset.RdThis function identifies potential metabolites in a `mass_dataset` object by matching MS1 and MS2 data with a reference spectral database. The function uses both MS1 (m/z) and MS2 (fragment ions) matching for more accurate identification.
metIdentify_mass_dataset(
object,
ms1.match.ppm = 25,
ms2.match.ppm = 30,
mz.ppm.thr = 400,
ms2.match.tol = 0.5,
fraction.weight = 0.3,
dp.forward.weight = 0.6,
dp.reverse.weight = 0.1,
rt.match.tol = 30,
polarity = c("positive", "negative"),
ce = "all",
column = c("hilic", "rp"),
ms1.match.weight = 0.25,
rt.match.weight = 0.25,
ms2.match.weight = 0.5,
total.score.tol = 0.5,
candidate.num = 3,
database,
threads = 3,
remove_fragment_intensity_cutoff = 0
)A `mass_dataset` object that contains MS1 and MS2 data.
A numeric value specifying the mass accuracy threshold for MS1 matching in parts per million (ppm). Defaults to `25`.
A numeric value specifying the mass accuracy threshold for MS2 matching in ppm. Defaults to `30`.
A numeric value specifying the m/z threshold in ppm for matching MS1 and MS2. Defaults to `400`.
A numeric value specifying the tolerance for MS2 fragment ion matching. Defaults to `0.5`.
A numeric value specifying the weight for the MS2 fragmentation score. Defaults to `0.3`.
A numeric value specifying the weight for the forward dot product in MS2 matching. Defaults to `0.6`.
A numeric value specifying the weight for the reverse dot product in MS2 matching. Defaults to `0.1`.
A numeric value specifying the retention time matching tolerance in seconds. Defaults to `30`.
A character string specifying the ionization mode. It can be either `"positive"` or `"negative"`. Defaults to `"positive"`.
A character string specifying the collision energy for MS2 matching. Defaults to `"all"`.
A character string specifying the chromatographic column type, either `"hilic"` (hydrophilic interaction) or `"rp"` (reverse phase). Defaults to `"hilic"`.
A numeric value specifying the weight of MS1 matching in the total score calculation. Defaults to `0.25`.
A numeric value specifying the weight of RT matching in the total score calculation. Defaults to `0.25`.
A numeric value specifying the weight of MS2 matching in the total score calculation. Defaults to `0.5`.
A numeric value specifying the threshold for the total score. Defaults to `0.5`.
A numeric value specifying the number of top candidates to retain per feature. Defaults to `3`.
A `databaseClass` object containing the reference spectral database for annotation.
An integer specifying the number of threads to use for parallel processing. Defaults to `3`.
A numeric value specifying the intensity cutoff for removing fragments in MS2 matching. Defaults to `0`.
A data frame containing the metabolite identification results, including m/z error, RT error, MS2 matching scores, and information about the identified compounds.
This function performs MS1 and MS2-based matching between the experimental data in the `mass_dataset` object and a reference spectral database. The matching process is based on mass-to-charge ratio (m/z), retention time (RT), and MS2 fragmentation patterns. The function supports both positive and negative ionization modes and can work with either HILIC or reverse-phase columns.
The matching process can be fine-tuned by adjusting the weights of MS1, MS2, and RT matching, as well as the tolerance parameters for m/z and MS2 matching.
if (FALSE) { # \dontrun{
# Perform MS1 and MS2-based metabolite identification in a mass_dataset object
identification_result <- metIdentify_mass_dataset(
object = mass_object,
ms1.match.ppm = 20,
ms2.match.ppm = 25,
rt.match.tol = 20,
database = reference_database,
threads = 4
)
} # }