View source: R/metIdentify_mass_dataset.R
metIdentify_mass_dataset | R Documentation |
Identify metabolites based on MS/MS database.
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
)
object |
A mass_dataset class object. |
ms1.match.ppm |
Precursor match ppm tolerance. |
ms2.match.ppm |
Fragment ion match ppm tolerance. |
mz.ppm.thr |
Accurate mass tolerance for m/z error calculation. |
ms2.match.tol |
MS2 match (MS2 similarity) tolerance. |
fraction.weight |
The weight for matched fragments. |
dp.forward.weight |
Forward dot product weight. |
dp.reverse.weight |
Reverse dot product weight. |
rt.match.tol |
RT match tolerance. |
polarity |
The polarity of data, "positive"or "negative". |
ce |
Collision energy. Please confirm the CE values in your database. Default is "all". |
column |
"hilic" (HILIC column) or "rp" (reverse phase). |
ms1.match.weight |
The weight of MS1 match for total score calculation. |
rt.match.weight |
The weight of RT match for total score calculation. |
ms2.match.weight |
The weight of MS2 match for total score calculation. |
total.score.tol |
Total score tolerance. The total score are refering to MS-DIAL. |
candidate.num |
The number of candidate. |
database |
MS2 database name or MS2 database. |
threads |
Number of threads |
remove_fragment_intensity_cutoff |
default is 0. |
A metIdentifyClass object.
Xiaotao Shen shenxt1990@outlook.com
The example and demo data of this function can be found https://tidymass.github.io/metid/articles/metid.html
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