Create a new motifset

Once MS2LDA experiments have been created and annotated, you could use them to create your own motifset on MotifDB. The patterns of fragments and neutral losses from these motifsets could be selected for unsupervised substructural discovery on new data when running LDA experiments on this website and on GNPS-MS2LDA workflow.

Create your own motifset on MotifDB from one of your own MS2LDA experiments

The following motif sets have been contributed by the community

Motifset Name	Feature Set	Description	No. motifs
Urine derived Mass2Motifs	0.005 Da	Mass2Motifs annotated from positive ionisation mode mass spectra generated from extracts of urine samples.	134 motifs
GNPS library derived Mass2Motifs	0.005 Da	MS/MS spectra obtained from reference compounds and isolated molecules from diverse sources with a focus on bacterial and plant related molecules - positive ionisation mode mass spectrometry on various instruments.	78 motifs
Massbank library derived Mass2Motifs	0.005 Da	MS/MS spectra obtained from reference compounds and isolated molecules from diverse sources with a slight focus on plant related molecules - positive ionisation mode mass spectrometry on various instruments	46 motifs
Rhamnaceae Plant Mass2Motifs	0.005 Da	Annotated Mass2Motifs from data set comprising 71 Rhamnaceae plant extracts	31 motifs
Euphorbia Plant Mass2Motifs	0.005 Da	Annotated Mass2Motifs from data set comprising 43 Euphorbia plant extracts	66 motifs
LDB_NEG_MotifDB_02	0.01 Da	Motif DB applicable to lichen samples, produced with 816 spectra from with 250 lichen molecules. The spectra were produced by three different machines (Agilent 6530 qToF, Waters Xevo G2-XS qToF, Thermo Orbitrap q-Exactive). The chemical classification of lichen compounds as described in Identification of lichen substances (Huneck & Yoshimura, 1996) was used to annotate the motifs produced. MS2LDA experiment used : 200421_LDB_NEG_07.	100 motifs
MIADB_pos_indole	0.005 Da	Motif DB applicable to MIA-containing plants, produced with 200 spectra from the MIADB - one annotated motif related to decorated indole substructures.	1 motifs
MIADB_pos_60	0.005 Da	Motif DB applicable to MIA-containing plants, produced with 200 spectra from the MIADB (60 mass 2 motifs)	7 motifs
MIADB_pos_100	0.005 Da	Motif DB applicable to MIA-containing plants, produced with 200 spectra from the MIADB (100 mass 2 motifs)	10 motifs
Streptomyces S29	0.005 Da	Mass2Motifs annotated from positive ionisation mode mass spectra generated from extracts of Streptomyces sp. S29 (Atacama Desert rhizosphere derived strain)	13 motifs
fragment_253.1925	0.005 Da	Common fragment from cholestane-like structures. Phytochem Anal. 2019 Mar;30(2):132-138. doi: 10.1002/pca.2798. Extending Compound Identification for Molecular Network Using the LipidXplorer Database Independent Method: A Proof of Concept Using Glycoalkaloids From Solanum Pseudoquina A. St.-Hil	0 motifs
Tps6_motifs	0.005 Da	Diatoms grown under phosphate-replete and phosphte-deplete conditions	1 motifs
LDB_NEG_MotifDB_01	0.005 Da	Motif DB applicable to lichen samples, produced with 1500 spectra from with 250 lichen molecules. The spectra were produced by three different machines (Agilent 6530 qToF, Waters Xevo G2-XS qToF, Thermo Orbitrap q-Exactive). The chemical classification of lichen compounds as described in Identification of lichen substances (Huneck & Yoshimura, 1996) was used to annotate the motifs produced. MS2LDA experiment used : 200326_LDB_NEG_02.	300 motifs
MIADB_pos	0.005 Da	Annotated Mass2Motifs from 200 monoterpene indole alkaloids from the MIADB (pos) Qtof	0 motifs
Streptomyces and Salinispora Mass2Motifs	0.1 Da	Annotated Mass2Motif set from Streptomyces and Salinispora extracts with 0.1 Da binned features	40 motifs
Photorhabdus and Xenorhabdus Mass2Motifs	0.005 Da	Mass2Motifs discovered in Molecular Networking clustered positive ionisation mode mass spectra generated from bacterial extracts of nematode symbionts of the Photorhabdus and Xenorhabdus genera.	46 motifs
LDB MotifDB POS	0.01 Da	MotifDB produced by the positive mode spectra of the LDB (250+ compounds with 745 spectra including different adducts and acquisition from three LC-MS instruments: Agilent 6530, Thermo Q-Exactive Focus, Waters Xevo G2-XS). Spectra were annotated with SMILES for MAGMa and substructure annotation. The chemical classes are from Huneck&Yoshimura (1996), and were used to annotate each motif. Parameters: 100 free motifs - binning of 0.01 Da.	100 motifs
Planomonospora-associated Mass2Motifs	0.005 Da	Annotated Mass2Motif set from Planomonospora extracts with 0.01 Da binned features.	30 motifs
Human Urine ESI_POS	0.005 Da	Mass2Motifs annotated from positive ESI ionization generated from urine samples.	0 motifs
20210810_16HT	0.005 Da	GNPS Analysis	0 motifs
test	0.005 Da	test	0 motifs
3C	0.005 Da	3C	0 motifs
3C10motif	0.005 Da	three standard1101	0 motifs
471	0.005 Da	2172	0 motifs
motif_interesting_72.081_45.05785	0.005 Da	Fregment_72.081_loss_45.057	0 motifs
cholestane_glicoalkaloids	0.005 Da	Common fragment from cholestane-like structures in glycoalkaloids. This is meant to include the key-fragments: 396.32 and 253.19 ([M+H]+. . Phytochem Anal. 2019 Mar;30(2):132-138. DOI: 10.1002/pca.2798. Extending Compound Identification for Molecular Network Using the LipidXplorer Database Independent Method: A Proof of Concept Using Glycoalkaloids From Solanum Pseudoquina A. St.-Hil	0 motifs
Test25	0.005 Da	Gg	0 motifs
Test	0.005 Da	Just a test	0 motifs

API access

MotifDB is accessible via an API.

The following instructions demonstrate how to interact with the API

http://m2slda.org/motifdb/list_motifsets will return a json dictionary that gives the names of available motif sets and their IDs.

To access a particular motifset, there are two options. Send a get request to http://ms2lda.org/motifdb/get_motifset/ID, where ID is the ID obtained from the motifset list will return a json object including all of the motifs in that motifset. Replacing get_motifset with get_metadata will return the metadata for those motifs.

Alternatively, if you want to get the motifs and metadata together for multiple motifsets, you can send a POST request to http://ms2lda.org/motifdb/get_motifset. Within the payload dictionary you should include a field motifset_id_list which holds a list of the IDs of the motifsets you'd like.

In addition, you will need to include a field called csrfmiddlewaretoken which holds a valid token. You can get one by sending a GET request to http://ms2lda.org/motifdb/initialise_api.

This way of getting motifs also allows you to filter duplicates. Simply add the field filter with the value "True" to your payload. The default filter threshold (cosine score) is 0.95. To change this, add a field "filter_threshold" to your payload.

Example

import requests

server_url = "http://ms2lda.org"

# Get the list of motif sets
output = requests.get(server_url + '/motifdb/list_motifsets')
motifset_list = output.json()

# Get a token
url = server_url + '/motifdb/initialise_api'
client = requests.session()
token = client.get(url).json()['token']

url = server_url + '/motifdb/get_motifset/'
data = {'csrfmiddlewaretoken': token}

# specify the name of motifsets of interest in motifset_list
massbank_motifset = 'Massbank library derived Mass2Motifs'
gnps_motifset = 'GNPS library derived Mass2Motifs'

massbank_id = motifset_list[massbank_motifset]
gnps_id = motifset_list[gnps_motifset]

# example - get the massbank and gnps motifsets
data['motifset_id_list'] = [massbank_id, gnps_id]
data['filter'] = "True"
data['filter_threshold'] = 0.95 # Default value - not required
output = client.post(url, data=data).json()
print 'Retrieved', len(output['motifs']), 'motifs', len(output['metadata'])

# example - get the massbank metadata only
url = server_url + '/motifdb/get_motifset_metadata/{}/'.format(massbank_id)
output = requests.get(url)
motif_metadata = output.json()
for k in motif_metadata.keys()[:5]:
    print k
    print motif_metadata[k]