Database construction

Construct in-house or public MS2 spectra database.

construct_database()

Construct in-house or public MS2 database for metid.

correct_database_rt()

Correct RTs of metabolites in database using internal standard list

get_ms2_spectrum()

Get MS2 spectra of peaks from databaseClass object

construct_massbank_database()

Construct public MS2 database from massbank with msp format.

construct_mona_database()

Construct public MS2 database from MoNA with msp format.

filter_adducts()

Filter adducts.

Metabolite identification

Metabolite identification based on MS1 and MS2 databases.

which_has_identification()

Get the peak names which have identifications

trans_to_new_style()

Transform old style identification table to new style

ms2plot()

Get MS2 match plots from a metIdentifyClass object

identify_single_peak()

Identify single peak based on database.

identify_metabolites_params()

Generate the parameter list for identify_metabolites function

identify_metabolites()

Identify metabolites based on MS1 or MS/MS database

get_parameters()

Get parameters from a metIdentifyClass object

get_ms2_spectrum_from_object()

Get spectra of peaks from metIdentifyClass object

get_identification_table()

Get identification table from a metIdentifyClass object

get_identification_table_all()

get_identification_table_all

get_iden_info()

Get identification information from a metIdentifyClass object

filter_identification()

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

annotate_metabolites_mass_dataset()

Identify metabolites based on MS1 or MS/MS database

annotate_single_peak_mass_dataset()

Identify metabolites based on MS1 or MS/MS database for single peak.

getIdentificationTable2()

Get identification table from a mzIdentifyClass object

getMS2spectrum()

Get MS2 spectra of peaks from databaseClass object

get_parameters_metid()

Get parameters from a metIdentifyClass object

identify_metabolite_all()

Identify metabolites using multiple databases one time

identify_ms2_only()

Identify metabolites based on MS/MS database

identify_peak()

Identify metabolites based on MS1 or MS/MS database

metIdentify()

Identify metabolites based on MS/MS database.

metIdentify_mass_dataset()

Identify metabolites based on MS/MS database.

ms2_plot_mass_dataset()

Identify metabolites based on MS1 or MS/MS database for single peak.

mzIdentify()

Identify peaks based on MS1 database

mzIdentifyParam()

Generate the mzIdentify parameter list

mzIdentify_mass_dataset()

Identify peaks based on MS1 database

mzIdentify_mass_dataset2()

Identify peaks based on MS1 database

Data

Some data embed in metid

hilic.pos

HILIC positive mode adduct table

hilic.neg

HILIC negative mode adduct table

rp.pos

Reverse phase positive mode adduct table

rp.neg

Reverse phase negative mode adduct table

msDatabase_hilic0.0.2

Michael Snyder lab RPLC database 0.0.2

msDatabase_rplc0.0.2

Michael Snyder lab RPLC database 0.0.2

orbitrap_database0.0.3

orbitrap_database0.0.3

snyder_database_hilic0.0.3

Michael Snyder lab RPLC database

snyder_database_rplc0.0.3

Michael Snyder lab RPLC database

Other functions

Other usefull functions in metid

readMGF()

readMGF

readMSP()

readMSP

readMZXML()

readMZXML

metid()

Show the base information of metid pacakge

metid_conflicts()

Conflicts between the metid and other packages

metid_logo()

Show the base information of metid pacakge

metid_packages()

List all packages in the metid

readMSP_MoNA()

readMSP_MoNA

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

colnames(<databaseClass>) nrow(<databaseClass>) ncol(<databaseClass>) dim(<databaseClass>)

colnames

summary_annotation_table()

Summary the annotation table

databaseClass-class

An S4 class to represent MS1 or MS2 database.

metIdentifyClass-class

An S4 class to represent annotation result.

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)