Man pages for tidymass/metid
Metabolite identification based on MS1 and MS2 spectra
| annotate_metabolites | Annotate Metabolites |
| annotate_metabolites_mass_dataset | Annotate Metabolites in a mass_dataset Object |
| annotate_peaks_mz_rt_ms2 | Annotate Peaks Based on MS1, Retention Time (RT), and MS2 |
| annotate_single_peak_mass_dataset | Annotate a Single Peak in a mass_dataset Object |
| calculate_confidence_level | Calculate Confidence Level for Metabolite Annotations |
| calculate_dotproduct | Calculate Dot Product Score for MS2 Spectra |
| calculate_ms2_matching_score | Calculate MS2 Spectra Matching Score |
| calculate_mz_match_score | Calculate m/z Match Score |
| calculate_rt_match_score | Calculate Retention Time (RT) Match Score |
| calculate_total_score | Calculate the Total Annotation Score |
| check_adduct_table | Validate the Adduct Table |
| check_database | Validate a Database Object for Metabolite Annotation |
| check_mass_dataset | Validate the mass_dataset Object for Metabolite Annotation |
| check_ms1_ms2_info | Validate MS1 and MS2 Information |
| check_parameters4annotate_metabolites | Validate Parameters for Metabolite Annotation |
| check_parameters4calculate_total_score | Validate Parameters for Calculating Total Score |
| construct_database | Construct a Mass Spectra Database |
| construct_massbank_database | Construct a Spectral Database from MassBank Data |
| construct_mona_database | Construct a Spectral Database from MoNA Data |
| correct_database_rt | Correct Retention Time (RT) in a Spectral Database |
| databaseClass-class | Class for Managing Spectral Database Information |
| extract_database_name | Extract the Name of the Database |
| extract_ms1_database | Extract MS1 Information from a Database |
| extract_ms1_info | Extract MS1 Information from a mass_dataset Object |
| extract_ms2_database | Extract MS2 Spectra from a Database |
| extract_ms2_info | Extract MS2 Information from a mass_dataset Object |
| filter_adducts | Filter adducts. |
| filter_identification | Filter identifications according to m/z error, RT error, MS... |
| get_iden_info | Get identification information from a metIdentifyClass object |
| get_identification_table | Get identification table from a metIdentifyClass object |
| getIdentificationTable2 | Get identification table from a mzIdentifyClass object |
| get_identification_table_all | get_identification_table_all |
| get_ms2_spectrum | Retrieve MS2 Spectrum from a Database |
| getMS2spectrum | 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 |
| 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_peak | Identify a Peak in a Mass Spectrometry Dataset |
| identify_single_peak | Identify single peak based on database. |
| load_adduct_table | Load the Adduct Table Based on Polarity and Column Type |
| match_ms2_fragments | Match MS2 Fragments Between Experimental and Library Spectra |
| match_ms2_temp | Match MS2 Spectra to Database Compounds |
| metid | Show the base information of metid pacakge |
| metid_conflicts | Conflicts between the metid and other packages |
| metIdentification | Metabolite Identification Using MS1 and MS2 Data |
| metIdentify | Identify metabolites based on MS/MS database. |
| metIdentifyClass-class | An S4 class to represent annotation result. |
| metIdentify_mass_dataset | Metabolite Identification in a mass_dataset Object Using MS1... |
| metid_logo | Display the metid Logo and Information |
| metid_packages | List all packages in the metid |
| ms2plot | Get MS2 match plots from a metIdentifyClass object |
| ms2_plot_mass_dataset | Plot MS2 Spectra for a Single Peak in a mass_dataset Object |
| msDatabase_hilic0.0.2 | Michael Snyder lab RPLC database 0.0.2 |
| msDatabase_rplc0.0.2 | Michael Snyder lab RPLC database 0.0.2 |
| mzIdentify | Identify peaks based on MS1 database |
| mzIdentify_mass_dataset | Metabolite Identification in a mass_dataset Object Using MS1... |
| mzIdentifyParam | Generate the mzIdentify parameter list |
| orbitrap_database0.0.3 | orbitrap_database0.0.3 |
| plot_ms2_matching | Plot MS2 Matching Between Experimental and Library Spectra |
| readMGF | readMGF |
| read_mgf_experiment | Read MGF Data from Experimental Files |
| read_mgf_gnps | This function reads Mass Spectrometry (MS) data in MGF format... |
| read_mgf_mona | Read MGF Data from MoNA |
| read_msp | Read MSP Data |
| readMSP | readMSP |
| read_msp_database | Read MSP Database |
| read_msp_gnps | —————– Read MSP Data from GNPS |
| read_msp_mona | —————– Read MSP Data from MoNA |
| readMSP_MoNA | readMSP_MoNA |
| readMZXML | readMZXML |
| reexports | Objects exported from other packages |
| remove_impossible_annotations | Remove Impossible Annotations Based on Adducts |
| remove_noise | Remove Noise from MS2 Spectrum |
| rp.neg | Reverse phase negative mode adduct table |
| rp.pos | Reverse phase positive mode adduct table |
| snyder_database_hilic0.0.3 | Michael Snyder lab RPLC database |
| snyder_database_rplc0.0.3 | Michael Snyder lab RPLC database |
| summary_annotation_table | Summary of Annotation Table with Plot |
| summary-databaseClass | colnames |
| trans_to_new_style | Transform old style identification table to new style |
| which_has_identification | Get the peak names which have identifications |
| write_mgf_gnps | Write GNPS Spectra to MGF Format |
| write_mgf_massbank | Write MassBank Spectra to MGF Format |
| write_mgf_mona | Write MoNA Spectra to MGF Format |
| write_msp | Write MSP Data to a File |
| write_msp_gnps | Write GNPS Spectra to MSP Format |
| write_msp_massbank | Write MassBank Spectra to MSP Format |
| write_msp_mona | Write MoNA Spectra to MSP Format |
