911.672

919.593

917.102

905.847

901.546

885.551

799.532871.571

913.687

937.584

797.516959.569

775.532

813.511

280.262

282.284

310.309

338.34

338.335

282.278

280.262

595.504953.58602.414

413.325

196.172

266.122

321.241317.1

196.169

196.169

196.169

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196.169196.169

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226.951

347.111

667.414

362.925

294.938

705.466

690.598

681.466

256.262

280.138

200.2

228.231

305.247

319.225

309.204

313.469

289.236

294.153

MetWork Documentation

v0.2.1

Grégory Genta-Jouve and Yann Beauxis

HTTPS://METWORK.PHARMACIE.PARISDESCARTES.FR

Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported License (the“License”). You may not use this file except in compliance with the License. You may obtain acopy of the License at http://creativecommons.org/licenses/by-nc/3.0. Unless requiredby applicable law or agreed to in writing, software distributed under the License is distributed on an“AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions and limitations under the License.

First printing, September 2018

http://creativecommons.org/licenses/by-nc/3.0

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Contents

1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51.1 General information 51.2 Data management 6

2 How to use MetWork? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92.1 Project creation 92.2 Results visualization 14

3 Reactions management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153.1 General information 153.2 Importing new reactions 16

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1. Introduction

1.1 General information

MetWork is a publically accessible web server for natural products anticipation (https:metwork.pharmacie.parisdescartes.fr). It is designed to be available through any web browser andcan be used with or without registration (using the "Guest" account).

Registration offers several benefits:• the data uploaded are not available to other user.• the data are stored and available without time duration limit.• an email is automatically sent to the user at the end of each run.• the user is informed of any upgrade or unavailability of the server.From the main page, it is possible to create an account by clicking on the green button "New

user".

It is important to know that your personal information will not be passed on to third partiesand that any modification can be realized from the "My account" panel. In any case and withoutjustification, a user can ask for a complete deletion of its account on the server by email to:metwork@pharmacie.parisdescartes.fr

https:metwork.pharmacie.parisdescartes.frhttps:metwork.pharmacie.parisdescartes.fr

6 Chapter 1. Introduction

1.2 Data managementThe current version of MetWork uses .mgf as input for the MS/MS data and .csv or .tsv forthe annotation. In order to be loaded on the server, each spectrum within the .mgf file must beidentified with a scan number ("SCANS="). Here is an example of a valid .mgf file containing onespectrum:

BEGIN IONSPEPMASS=239.16319CHARGE=1+MSLEVEL=2FILENAME=demo.mgfRTINSECONDS=1799.800049INSTRUMENT=ion trapTITLE=Scan Number: 1SCANS=1105.046028 29.035715106.778130 6.062500109.104729 25.778847111.032387 21.625000115.332619 5.000000115.902672 5.160714117.066956 25.005953120.138046 16.562500END IONS

BThe .mgf file must contain more than one spectrum in order to be used in a project.The data upload is performed from the "My Data" panel.

A single click on the green button "Import File" will open a pop-up window in which the pathof the .mgf file can be selected.

1.2 Data management 7

The total ion number limit for one .mgf file is 20000 (if the number of ions in the file exceedsthis limit, an error message will appear). It is possible to monitor the processing of the file in realtime. The dataset name in italic indicates than the loading is still going on and the dataset can’t beused. The number of spectra already processed is also displayed.

As already stated, annotation files can be uploaded to the server under two formats from the"Annotations" panel.

The first one is a comma delimited .csv file that contains five columns (nodeId,name,smiles,source,sourceId).Here is an example of a valid .csv file:

IonId,name,smiles,source,sourceId1,my_compound_name,OC(C=C1)=C(O)C=C1C2=CC3=CC(O)=CC=C3C=C2,My Database, GGJ-0001

Another option is to use the .tsv file generated by the GNPS platform (https://gnps.ucsd.edu). The choice can be specified during the upload by selecting the file format in the pop-up.

https://gnps.ucsd.eduhttps://gnps.ucsd.edu

8 Chapter 1. Introduction

Once loaded, the annotation information are displayed on the "Annotations" panel.

The last feature of the "My Data" panel is the ability to generate a molecular network. Thisoption is available on the "Network" panel. The network can be generated by click on the navyblue button "load network".

BDepending on the number of ions in the .mgf file, the loading time can be long has itis calculated by the browser i.e. the user machine.

The annotated nodes appear in color, green nodes are the ones from the annotation file, if aproject associated to this dataset has already been run, some in-silico predicted compounds canappear in orange on the network. More details on how to create a project will be given in thefollowing section.

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2. How to use MetWork?

2.1 Project creation

The use of MetWork is based on the creation of a project that contains three elements:• a dataset• an annotation for at least one spectrum in the dataset• a set of reactions (minimum 1) to be used during the metabolization

In order to create a new project, the user have to go on the panel "My Projects" in the main menu.A simple click on the green button "New project" gives the new project creation form. By default,

the project name is New project followed by the current date and time. This can be changed beforeclicking on the button "Create project" or edited later.

Once created, a project status is defined and displayed next to the project name. Several projectstatus can be set depending on the current state of the project creation and completion. The statuscan be:

• Initialized (gray): the project has just been created and some parameters have to be definedin order to be run.

10 Chapter 2. How to use MetWork?

• Ready to run (sky blue): all the mandatory information are given and the project is ready forrun.

• Queued (orange): the project has been submitted to the server but is not being processed yet.• Running (orange): the project is being processed by the server.• Finished (navy blue): the project has been processed and the results are available.

At this stage, the project can be edited and a description can be added. After any changes inthe text (Name or description), a click on "Save Info" is necessary. The next step consists in thedata selection (MS/MS data). The data used in the project will be selected from the panel "Data"after one click on "Select data". A pop-up with all available datasets will show up and display thenumber of ions and the number of annotation(s).

Just after the data selection, it is possible to select/deselect the annotated ions to be used duringthe metabolization step. The ions selected are displayed on the left column (selected) while the

2.1 Project creation 11

unselected ions are displayed on the right column (available).

It is then necessary to define the depth of metabolization parameters and the list of reactions.All of this is to be accomplished from the "Metabolization panel".

BIt is important to press "Save" after having set the depth of metabolization.The comparison of theoretically predicted and experimental MS/MS spectra is performed using

the cosine score calculation. The cosine threshold can be changed in the "Fragmentation" panel.Some other parameters can be changed as well (e.g. cosine m/z tolerance).

12 Chapter 2. How to use MetWork?

BIt is important to press "Save" after having set the cosine threshold.When all the mandatory information are given (data, annotation, metabolization depth and

reaction), the status of the project is "Ready to run" (on the "Info" panel).

A simple click on the "Start run" will launch the project and the project status will change to"Running" (or "Queued" if other tasks are already processed by the server). During the run, the

number of molecules generated is displayed as well as the number of annotations.At the end of the run, the status changes to "Run finished" on the "Info" panel (If registered, an

email is sent to the user at the end of the run). All the results can be downloaded from the "Info"panel. Four files are available:

• Annotations : metwork_annotation.csv contains a list of annotated MS/MS spectra(nodes) for which only one annotation per node is given (the highest cosine score).

• Annotation details (metwork_annotation_details.csv) : contains a list of annotatedMS/MS spectra (nodes) for which all possible annotations per node is given (all cosine scoresare available).

• MetExplore (metwork_metexplore.json) : contains the metabolization network of all

2.1 Project creation 13

annotated spectra. This file can be opened using the MetExploreViz plug in available on theMetExplore web-site (https://metexplore.toulouse.inra.fr/metexplore2/)

• All molecules (metwork_all_molecules.csv) : contains the structure of all generatedcompounds of the project.

The results can also be displayed on the MetWork web-page using the visualization interface.More details are given in the following section.

https://metexplore.toulouse.inra.fr/metexplore2/

14 Chapter 2. How to use MetWork?

2.2 Results visualizationAt the end of the run (project status "Run finished"), the metabolization network can be loadedwithin the "Metabolization" panel. Depending on the network size the loading can take some time.When loaded, the network is drawn. As seen on the figure below, two colors are used for the nodes,green and orange. The green one correspond to the annotation information given by the user whenuploading the dataset. The orange nodes are in-silico generated structures produced by MetWork.By clicking on the "Display cosines" button, cosine values can be displayed on the nodes.

It is also possible to click on the nodes in order to draw the chemical structure of the corre-sponding compound. Another feature of the visualization tool is the ability to select subnetwork byclicking on the compounds or reactions nodes (long click of 3 s). As shown in the example below,it is possible to visualize the direct connection between the anchor node (green) and the producedmetabolites with the cosine value of 0.294. It is also possible to reload the entire network using therefresh button on the top right corner.

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3. Reactions management

3.1 General information

The current version of MetWork uses Reactor (ChemAxon) for the in-silico metabolization of thecompounds uploaded by the user. The standard format for Reactor is .mrv and this is the formatused for the implementation of new reactions on the MetWork server. When necessary, a newreaction can be created using the Reactor interface as presented below.

For more information, we invite the user to read the Reactor’s documentation on the ChemAxonwebsite (https://chemaxon.com/products/reactor).

https://chemaxon.com/products/reactor

16 Chapter 3. Reactions management

3.2 Importing new reactionsThe upload of new reaction files is located on the "Reactions" panel where are listed all availablereactions. It is important to remember that all reactions are shared between all users, i.e. onceuploaded, any user can select one or more reactions of the database.

To add a new reaction file, a single click on the green button "Import File" will open the uploadpop-up.

At the end of the processing, the reaction will appear in the list of reactions. All reactionsare alphabetically ordered. It is possible to edit the description of the reaction by clicking on thereaction name in the list. A reaction page will appear and show reaction details such as name,number of reactants, description and a graphical representation.

It is possible to test if the reaction has been correctly processed by the server using the test

3.2 Importing new reactions 17

section located in the left bottom of the panel. After having entered a SMILES, the user cangenerated a new compound by clicking on the navy blue button "Run reaction".

On the bottom right will appear the newly created structure as a SMILES. When multipleproducts can be created, one SMILES per line will appear.

1 Introduction1.1 General information1.2 Data management

2 How to use MetWork?2.1 Project creation2.2 Results visualization

3 Reactions management3.1 General information3.2 Importing new reactions