Function reference • MS2extract

All functions

CE_filter(): Filter Collision Energy Values

add_attributes(): Evaluate additional .msp fields

assign_scan_id(): Extract MS/MS spectrum info out of the list

batch_detect_mass(): Detect masses for multiple spectra

batch_extract_MS2(): Extract the most MS/MS intense scan from batch spectra

batch_import_mzxml(): Batch import mzxml files

check_MS_data_order(): Check if spec MS/MS data and spec_metadata is proper aligned

check_gnps_metadata(): Checking names in the provided GNPS metadata

check_metadata(): Check compound metadata

check_specdt_mgf_gnps(): Check spec_metadata for GNPS .mgf format before exporting the MS/MS library

check_specdt_msp(): Check spec_metadata for NIST format before exporting the MS/MS library

compare_spectra(): Compare two MS/MS spectra based on cosine score

detect_mass(): Detect masses in a MS/MS spectra

extract_MS2(): Extract the most intense MS/MS scan

extract_scan_info(): Extract scan info out of the list

get_TIC(): Calculate the total ion chromatogram (TIC)

get_ppm(): Calculate the m/z difference for a given mass and ppm tolerance

import_mzxml(): Imports mzXML/mzML files with MS/MS scans

mgf_GNPS_core(): Writes the GNPS .mgf backbone

normalize_spec(): Normalization and low intensity signal filtering

plot_MS2base(): Base function for MS2 spectra

plot_MS2spectra(): Plot MS/ms spectra

plot_tic(): Plot MS/MS TIC

ppm_range(): Calculate the m/z upper and lower values limits given a ppm tolerance

read_mzxml(): Read .mzxml/.mzML files containing MS/MS data

roi_filter(): Filtering the region of interest (ROI)

sort_compound_table(): Sort compound table before importing data

write_gnps_table(): Creates the batch upload .tsv table for GNPS batch upload job

write_mgf_gnps(): Create the GNPS .mgf backbone file format

write_msp(): Export MS/MS spectra to a .msp file

write_msp_base(): Export MS/ms spectra to a .msp file