1.      After uploading the HDX file, I get an error message. How do I fix it?

This happens when the input information of your experiment does not match the uploaded .csv file. Please carefully review your input data and try again. IMPORTANT: Please make sure your data have the same number of replicates for all peptides.

2.      The woods plot shows peptides coloured yellow. Are those peptides significant?

Those peptides are considered significant after running the hybrid significant test. They are coloured yellow because individual timepoint within the peptide showed both increase and decrease flexibility at the same time. We recommend the user to go back to the raw data and re check the quality of the data for that peptide.

3.      I am using multiple protein states. Can I run the statistical analysis using all the protein states at the same time?

No, although in most cases having more proteins states might improve the pooled standard deviation calculation, if one those protein states have an abnormal standard deviation, the calculated pooled standard deviation will be higher provoking less peptides to be considered significant. As a result, we decided to use only the two states involved in the differential experiment for the statistical analysis. We invite you to check the code and modify it yourself if you want a different statistical approach.

4.      When is a peptide considered significant?

The hybrid significance test evaluates both the statistical significance and the magnitude of the changes for individual differences. As a result, for a given peptide you will have as many statistical tests as labelling time points. For the purpose of this app, a peptide is considered significant when at least one of the individual comparisons is significant by the hybrid significant test.

In rare cases, individual differences within the same peptide show both increase flexibility and increased protection at different labelling times. In these cases, we recommend the user to go back to the raw data and curate it again to ensure this phenomenon is not due to peak misalignment or abnormal standard deviations.

5.      Who should I contact to report bugs or suggestions?

Please refer to the About tab in the left side menu.