All functions

annotate_result

A metIdentifyClass object.

construct_database()

Construct in-house or public MS2 database for metID.

construct_massbank_database()

Construct public MS2 database from massbank with msp format.

construct_mona_database()

Construct public MS2 database from MoNA with msp format.

correct_database_rt()

Correct RTs of metabolites in database using internal standard list

databaseClass-class

An S4 class to represent MS1 or MS2 database.

databaseConstruction()

Construct in-house or public MS2 database for metID.

filterIden()

Filter identifications according to m/z error, RT error, MS similarity and total score

filter_adducts()

Filter adducts.

filter_identification()

Filter identifications according to m/z error, RT error, MS similarity and total score

getIdenInfo()

Get identification information from a metIdentifyClass object

getIdentificationTable()

Get identification table from a metIdentifyClass object

getIdentificationTable2()

Get identification table from a mzIdentifyClass object

getMS2spectrum()

Get MS2 spectra of peaks from databaseClass object

getMS2spectrum2Object()

Get spectra of peaks from metIdentifyClass object

getParams()

Get parameters from a metIdentifyClass object

getParams2()

Get parameters from a mzIdentifyClass object

get_iden_info()

Get identification information from a metIdentifyClass object

get_identification_table()

Get identification table from a metIdentifyClass object

get_identification_table_all()

get_identification_table_all

get_ms2_spectrum()

Get MS2 spectra of peaks from databaseClass object

get_ms2_spectrum_from_object()

Get spectra of peaks from metIdentifyClass object

get_parameters()

Get parameters from a metIdentifyClass object

get_parameters_metID()

Get parameters from a metIdentifyClass object

hilic.neg

HILIC negative mode adduct table

hilic.pos

HILIC positive mode adduct table

identifyPeak()

Identify metabolites based on MS1 or MS/MS database

identify_metabolite_all()

Identify metabolites using multiple databases one time

identify_metabolites()

Identify metabolites based on MS1 or MS/MS database

identify_metabolites_params()

Generate the parameter list for identify_metabolites function

identify_ms2_only()

Identify metabolites based on MS/MS database

identify_single_peak()

Identify single peak based on database.

metID()

Show the base information of metID pacakge

metID_logo()

Show the base information of metID pacakge

metIdentify()

Identify metabolites based on MS/MS database.

metIdentify4all()

Identify metabolites using multiple databases one time

metIdentifyClass-class

An S4 class to represent annotation result.

metIdentifyParam()

Generate the parameter list for metIdentify function

ms2plot()

Get MS2 match plots from a metIdentifyClass object

msDatabase_hilic0.0.2

Michael Snyder lab RPLC database

msDatabase_rplc0.0.2

Michael Snyder lab RPLC database

mzIdentify()

Identify peaks based on MS1 database

mzIdentifyParam()

Generate the mzIdentify parameter list

readMGF()

readMGF

readMSP()

readMSP

readMSP_MoNA()

readMSP_MoNA

readMZXML()

readMZXML

read_mgf()

read_mgf

read_mgf_experiment()

read_mgf_experiment

read_mgf_gnps()

read_mgf_gnps

read_mgf_mona()

read_mgf_mona

read_msp()

read_msp

read_msp_database()

read_msp_database

read_msp_gnps()

read_msp_gnps

read_msp_mona()

read_msp_mona

read_mzxml()

read_mzxml

rp.neg

Reverse phase negative mode adduct table

rp.pos

Reverse phase positive mode adduct table

trans2newStyle()

Transform old style identification table to new style

trans_to_new_style()

Transform old style identification table to new style

whichHasIden()

Get the peak names which have identifications

which_has_identification()

Get the peak names which have identifications

write_mgf_gnps()

Export metID database to mgf (gnps format)

write_mgf_massbank()

Export metID database to mgf (MassBank format)

write_mgf_mona()

Export metID database to mgf (mona format)

write_msp_gnps()

Export metID database to msp (gnps format)

write_msp_massbank()

Export metID database to msp (MassBank format)

write_msp_mona()

Export metID database to msp (mona format)