Protocol

Study Protocols

Protocols are central for reproducibility purposes and should provide a detailed description of the steps taken in the study. When an assay is selected, the protocol section will populate with several titled sections which you can add your specific study details to.

Example

Eg. Liquid chromatography - Mass Spectrometry

1. Sample collection Describe the origin of samples, any relevant treatment, time points etc. and the collection and storage procedure.

2. Extraction Describe any extraction or preparation methods applied to the sample before analysis. Please also include any control samples prepared for the assay eg. pooled samples, standards, quality control, solvent blank etc

3. Chromatography Provide details of the instrument and column used (make & manufacturer), mobile phase and gradient, and settings such as temperatures, flow rate, injection volume.

4. Mass spectrometry Provide details of the instrument used (make & manufacturer), ion source, ionisation mode (positive / negative), m/z range, and specific parameters such as temperatures, voltages, flow rates, scan rates.

5. Data transformation Provide details of methods / pipelines and software used to transform the raw data.

6. Metabolite identification Provide details of methods / pipelines, reference databases and software used to identify features and/or annotate metabolites.

Validation rules

• The protocol should be at least 40 characters long.

• The protocol name should be at least 8 characters long.

• All expected protocol should be defined.

• All characters should be printable in the protocol description, ie. non-UTF-8 compatible characters.