Usage

On the 'Start Analysis' page, new FERMO analysis jobs can be initiated.

Files can be uploaded using the individual upload fields. The analysis job can be started by clicking on the 'Start Analysis' button at the bottom of the page.

The only file required is a peaktable file - all other files are optional.

While default parameters are provided, they need to be adjusted according to the requirements of the data.

Nota bene: FERMO online versions employs some restrictions with regard to file size, computation time, and data storage to prevent excessive usage. Details can be found on the 'Start Analysis' page.

Example

Load parameters

This field allows to clone the parameter settings of a previous FERMO job (e.g. created by a colleague).

To load the parameters, simply paste the FERMO job ID into the field, and click on the 'Load Job Parameters' button.

Nota bene: files and filenames are not retained and must be newly uploaded.

Example

Troubleshooting

If an old job ID does not exist anymore but you still want to clone the parameters, you can simply upload a previously created FERMO session.json file under Load Session. Take the newly generated FERMO job ID and use it to load the parameters.

Peaktable

The peaktable is the only file that is mandatory for analysis.

See here for more information on the required peaktable format.

MS/MS

(optional)

Availability of MS/MS data is very important for annotation tasks. If MS/MS data is available, it is highly recommended to include such a file in the analysis. However, even if MS/MS data is provided, usually not all molecular features have associated MS/MS information, and FERMO will ignore such features in annotation tasks requiring MS/MS data.

See here for more information on the required MS/MS file format.

By default, FERMO performs quality-filtering of MS/MS fragments. See here for additional information.

Group Metadata

(optional)

Group Metadata allows to provide sample context information. Using sample grouping, the abundance of features across groups (area, intensity) can be compared. Additionally, sample blanks can be designated to identify background ions.

See here for more information on the required Group Metadata file format.

Phenotype Data

(optional)

Phenotype data allows to correlate feature abundance with a phenotype/bioactivity signal. FERMO supports three different data formats/strategies:

• qualitative phenotype data
• percentage activity-based quantitative data
• concentration-based quantitative data

See here for more information on the required Phenotype Data file format.

Spectral Library

(optional)

FERMO accepts a user-provided spectral library for feature annotation. Spectral library matching can be performed with two different algorithms:

• Modified Cosine: Ideal to detect close similarity.
• MS2DeepScore: Can detect also distant similarity.

Ideally, a library targeted towards the research question/organism is used. This can help to reduce the chance of non-sensical spurious hits (e.g. matching of human metabolites against a bacterial dataset.)

See here for a collection of different spectral libraries.

See here for more information on the required Spectral Library file format.

MS2Query Annotation

(optional)

FERMO accepts result files coming from the MS2Query annotation program. While previous versions of FERMO employed an inbuilt version of MS2Query, this has been discontinued due to integration issues. Therefore, MS2Query needs to be run separately by the user.

See here for more information on the required MS2Query results file format.

antiSMASH Job Integration

(optional)

FERMO can also integrate results coming from the popular genome mining software antiSMASH. For this, FERMO requires only an existing antiSMASH job ID.

Keep in mind that only a single genome is used for annotation. In this case, all samples are assumed to result from organism the genome is associated with.

See here for more information on the annotation logic.

See here for more information on the expected format.

Notification Settings

(optional, only in online mode)

If an email address was provided, a notification will be sent on job completion (success or failure).