Package index

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