metID.dbAnnotate: Annotate unknown features in a compMS2 class object to...

In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

unknown metabolite identification. MS1 features within a compMS2 object are matched against a metabolite database based on a mass accuracy tolerance (ppm). Possible electrospray adducts/ in-source fragments and substructure mass shifts are calculated for all data base entries. Substructure mass shifts are supplied as a named numeric vector or default is all the mass shifts in the internal substructure masses table (see default Substructure_masses). Custom ESI adduct/ in-source fragments can be supplied as a character string of names or the output of the function adduct2mass. See examples.

Usage

metID.dbAnnotate(object, ...)

Arguments

object	a compMS2 class object.
ppm	numeric mass accuracy error (ppm) to match MS1 features to data base entries.
esiAdducts	data.frame or character vector of custom electrospray adducts can be supplied as a character vector of electrospray adducts or as a data.frame output from the function adduct2mass. e.g. c("[M-H-NH3-CO-COCH2-C4H6O]-", "[4M-H+Cl]2-", "[2M-H]-", "[3M-3H+Fe2+]-", "[M-H-CH2O]-", "[3M-2H]2-", "[M-H-CO2-C3H6]-", "[M-H+CH3COOH]-", "[3M-H]-", "[M-2H]2-")
metDB	a metabolite data base (see default ?HMDB for table format). Other currently available data bases include LMSD, DrugBank, T3DB and ReSpect databases. Matching using multiple databases is also possible.
SubStrs	named numeric vector of substructure mass shifts to consider. If argument is not supplied then no substructure mass shifts will be considered. If the character "All" is supplied then all the substructure mass shifts contained in the internal table will be considered (see default Substructure_masses for more information).
featureSubSet	character vector of composite spectra names (e.g. CC_1, CC_2 etc.) otherwise the default is to perform database annotation on all composite spectra.
includeElements	character vector of element symbols (case-sensitive) to include in the metDB argument. Any structure containing an element which is not in this inclusion list will not be considered. see ?exactMassEle for the internal element table.
mixtures	logical (default = FALSE), should mixtures be considered. Any SMILES codes consisting of multiple non-covalently linked structures will not be considered (e.g. salts)
MS1adducts	logical (default = FALSE), should the adducts included in the 4th column of the MS1feature table be used to reduce false positive assignments. The adducts identified will be used to guide the annotation process, only the unique adducts/fragments will be used to calculate the expected mass shift values. If a spectrum has no adduct identified then all of the unique adducts identified in the dataset will be used.

Value

a compMS2 class object containing potential metabolite annotations.

References

1. Stanstrup, J., Gerlich, M., Dragsted, L.O. et al. Anal Bioanal Chem (2013) 405: 5037. doi:10.1007/s00216-013-6954-6

See Also

adduct2mass.

Examples

SubStrMassShift <- c(42.010565, 119.004101, 176.03209, 255.988909, 305.068159, 
                     57.021464, 161.014666, 79.956817)
names(SubStrMassShift) <- c("acetyl", "cysteine", "glucuronide", 
                            "glucuronide sulfate", "glutathione", "glycine",
                            "mercapturate", "sulfate")
# custom ESI adducts (default is to consider all ESI adducts/ in-source 
# fragments from supplementary material Beyond Profiling manuscript 
# see references for details)
# The function adduct2mass can interpret ESI adduct names and generate a 
# data.frame of expected mass shifts
customEsiAdducts <- c("[M-H-NH3-CO-COCH2-C4H6O]-", "[4M-H+Cl]2-", "[2M-H]-", 
                      "[3M-3H+Fe2+]-", "[M-H-CH2O]-", "[3M-2H]2-", 
                      "[M-H-CO2-C3H6]-", "[M-H+CH3COOH]-", "[3M-H]-", 
                      "[M-2H]2-")

compMS2Example <- metID(compMS2Example, "dbAnnotate", SubStrs=SubStrMassShift, 
                        esiAdducts=customEsiAdducts)
                                      

WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.