Tutorial

Quick Search

Search by CropMetaWeb ID, compound name, SMILES, molecular formula, and InChI.

You can input key fields of data entries including ID (Metabolite ID or compound ID), Name, Formula, InChI or SMILES in the search bar for quick search. The sub-query box will provide some options to search in metabolites, pesticides, compounds, and spectrum libraries in CropMetaWeb.

Browse

The ‘Browse’ module is designed for users to browse crop metabolites and compound data. Users can browse the webservice via clicking the "Browse" button on the homepage, and then access specific data via multiple options. Each data entry assigned unique CropMetaWeb identifiers has a dedicated summary information card and detailed information page. And users can access entries of their interest quickly by a sub-query box on the browsing page.

1 Browse metabolites for each crop

User can click on a specific column on the "Crop Metabolites" bar to access the metabolites have been identified from the corresponding crop. A new webpage will be shown to present a table that contains metabolites matched on you click. This table includes metabolite ID, molecular formula, molecular weight, SMILES and database. Detailed information of specific metabolites can be accessed by clicking the "Display full record".

2 Browse compound and structure

User can click on a specific column on the " Compound and structure" bar to view property information for the bioactive compounds and pesticidal compounds collected from databases. On the display page that can provide you with detailed information about each compound. Detailed information of specific compound can be accessed by clicking the "Display full record".

Search

In the Searching metabolites module under “Discover”, users are able to specify the domain you want to query. You can search by structure, compound weight range or advanced query to access metabolites and pesticides.

1 Structure Query

Users you can draw a molecular structure on this page and then do an exact search to find records of related metabolites and pesticides.

2 Molecular Weight Query

The molecular weight query allows user to set the range of the molecule weight of interest to find records of related metabolites and pesticides.

3 Advanced Query

Advanced Query enables users to search for a metabolite or pesticide of their interest by specifying structural properties and molecular descriptors. Users can use one or combination of multiple of these options in "Name, Molecular Formula, ID, SMILES, InChI, Metabolite Class, Crop Species" to customize their search. After clicking the "Search" button, a new webpage will display matched metabolites and pesticides.

Metabolite identification

The metabolite identification module under “Discover” of CropMetaWeb provides users with three powerful tools for crop metabolite identification.

1 MS2Tblast

MS2TBlast allows users to search against a MS2T library of chosen crop species uses one or multiple m/z values of precursor ions. Clicking the "Load Sample" button will automatically fill in a sample data. In this tool, one or multiple m/z values of precursor ions from sample MS spectra are manually entered in the text box. Then users can set the parameter of m/z tolerance, ion mode, and sample species, before query is executed by clicking the ‘search’ button.

2 CompoundLibBlast

CompoundLibBlast allows users to use MS1 data (Parent Ion m/z) and MS2 data (Fragment Ions m/z and Intensity values) entered, to search against either the experimental spectral library (default), or both the experimental spectral library and the in silico spectral library (check select box). Clicking the "Load Sample" button will automatically fill in a sample data. Notably, in the returned results, the matched records are ordered with the similarity scores computed using the INCOS algorithm. It returns all matched reference compounds for the paired MS1/MS2 data of your interest.

3 FlavoBLAST

FlavoBLAST allows users to use MS1 data (Precursor Ion m/z) and MS2 data (Fragment Ions m/z) that enter for the suspected precursor compounds, to search against the in-source fragment ions in the library of flavonoid motifs combined with neutral losses. Clicking the "Load Sample" button will automatically fill in a sample data. Results will be returned all matched flavonoids or flavonoid derivatives for the paired MS1/MS2 data after executing the query by clicking the "Search" button.

Sample analysis

The metabolite identification module under CropMetaWeb "Discover" will be a good choice if you want to perform metabolite annotation or pesticide detection in crop sample.

1 CropMetaDiscover

For a sample LC-MS datafiles in standard formats (mzML, mzXML, or mzData), CropMetaDiscover function allows users apply our pipeline to perform metabolite annotation on the sample. You need to fill in the contact information and set the parameters for ion mode and the crop species accurately. Once the data is submitted and the analysis is complete, a web link (valid for 72 hours) to a result page will be returned by email. Users can use to retrieve the annotation results that include statistics of annotated peaks, categories of identified metabolites, and downloadable files for all extracted MS/MS spectra, and annotation of non-redundant peaks.

2 PesticiSCAN

PestsiciSCAN allows users to detect pesticide residues on the samples apply our pipeline. Like the CropMetaDiscover page, users need to fill in the information of the Data upload portal carefully and a web link (valid for 72 hours) to a result page will be returned by email.

Repository

CropMetaWeb as a public repository for sharing crop metabolomics data and users can freely and easily download raw data. In the webpage of “Repository” module, there is a download summary table that includes several data sections users can filter depends on their interest.

Submit

In order to submit metabolomics data for CropMetaWeb, you need to be first filled project-sample-metadata file and request a Project_ID by email. Your email will not be replied immediately, but after they have been confirmed by a reviewer. Once a Project_ID is assigned to you by email, you will be able to submit new data files, or update existing data files under the project you own. Your raw data will be found in “Repository” module within 15 days after you submit.

Please do not use the "back" and "forward" button of your browser while doing a submit. After click on the "Submit " tab, you will see a progress bar for uploading data. If for some reasons your submit is interrupted, you can continue that in next time. You will see a green box on the new webpage where you can choose to continue to submit and this page will prompt the data files have been uploaded successfully.