Start analysis

Upload your data, set your preferred parameters, and you are good to go! You can also reload the parameter settings of your previous job and use them to run a new analysis.

Attention Online Users!

The online version of FERMO has a few restrictions due to computational restrains and to keep the service broadly accessible:

A file size limit of 9 MB, with a maximum of 3000 molecular features in the peaktable.
A maximum total job run time of 60 minutes.
The maximum job storage time is limited to 30 days. Make sure to download your results!

To bypass these restrictions, you can install and run FERMO offline.

Select one of the following options to start your FERMO analysis:

Start new analysis Load parameter settings Load results of previous session

FERMO session reload

FERMO parameter settings reload

Peak table file parameters

Upload the peak table file (.csv)

Select the formatting of the peak table file

Select the ion polarity mode of the peak table file

Feature Filtering Module

Specify parameters

Filter Feature Area

Range of relative feature areas to include in analysis

min

max

Filter Feature Height/Intensity

Range of relative feature height/intensity to include in analysis

min

max

Adduct Annotation Module

Specify parameters

Mass accuracy tolerance (in ppm)

MS/MS file parameters

Upload the MS/MS file

Select the formatting of the MS/MS file

Minimum relative intensity of MS/MS fragments

Neutral Loss Annotation Module

Specify parameters

Mass accuracy tolerance (in ppm)

MS/MS Fragment Annotation Module

Specify parameters

Mass accuracy tolerance (in ppm)

Spectral/Molecular Networking (Modified Cosine) Module

Specify parameters

Filters min nr of fragments per MS/MS spectrum

Fragment matching tolerance (in m/z)

Score cutoff for match

Max nr of edges of any node

Spectral/Molecular Networking (MS2DeepScore) Module

Specify parameters

Filters min nr of fragments per MS/MS spectrum

Score cutoff for match

Max nr of edges of any node

Phenotype data file parameters

Upload the phenotype data file (.csv)

Select format of phenotype data file

Specify parameters Qualitative

Min fold difference active/inactive

Algorithm for fold calculation

Value for fold calculation

Specify parameters Quantitative-percentage

Duplicate phenotype measurement averaging

Feature property to use for correlation

Correlation algorithm

False discovery rate correction

Corrected p value threshold

Correlation coefficient r threshold

Specify parameters Quantitative-concentration

Duplicate phenotype measurement averaging

Feature property to use for correlation

Correlation algorithm

False discovery rate correction

Corrected p value threshold

Correlation coefficient r threshold

Sample metadata file parameters

Upload the sample group metadata file (.csv)

Select the formatting of the sample group metadata file

Group Factor Assignment Module

Specify parameters

Algorithm for fold calculation

Value for fold calculation

Blank Assignment Module

Specify parameters

Min fold difference blank/sample

Algorithm for fold calculation

Value for fold calculation

Feature identity annotation parameters

Spectral Library Annotation Module

Specify parameters

Upload spectral library files (.mgf)

Select the formatting of the spectral library files

Modified Cosine Matching Module

Specify parameters

Min nr of matched MS/MS fragments

Fragment matching tolerance (in m/z)

Score cutoff for match

Max difference between precursor m/z

MS2DeepScore Matching Module

Specify parameters

Score cutoff for match

Max difference between precursor m/z

AntiSMASH Annotation Module

Specify parameters

Specify antiSMASH Job ID

KnownClusterBlast Similarity Cutoff (=%)

Modified Cosine Matching Module

Specify parameters

Min nr of matched MS/MS fragments

Fragment matching tolerance (in m/z)

Score cutoff for match

Max difference between precursor m/z

MS2DeepScore Matching Module

Specify parameters

Score cutoff for match

Max difference between precursor m/z

MS2Query Annotation Module

Specify parameters

Upload the MS2Query results file (.csv)

MS2Query Match Score Cutoff

Provide an email to be notified about the job outcome (optional)