Proteolabels 1.0 User Guide


Troubleshooting

No results found by search

This issue will generally occur if either your search was incorrect or the features were mis-identified. Firstly, ensure your search parameters are correct - it is necessary to do this even if auto-detect is used. Ensure first and foremost the correct labels are assigned to the correct channel with the appropriate shift. Specifically you should provide at least 2 digits of precision when specifying mass shifts. Incorrectly specifying these values may result in correct data being rejected due to a low mass shift tolerance value.

To ensure your tolerances are correct it is useful to increase the mass shift and retention time tolerance to a wider value, e.g. 100ppm and 2 minutes respectively, and then review the delta plots once data is found. If after you widen the tolerance values and still no data is found then this indicates you have an error in your choice of labels or in your identification search.

No identifications in data

This issue is caused by either:

1) If no identifications are shown at all on the identification panel, then you have imported data from Progenesis without first completing the identify peptides stage. Prior to exporting data to Proteolabels you will need to identify your data and import the identifications in to Progenesis. You should re-complete this stage in Progenesis and then re-execute the export to Proteolabels.

2) If your identifications are shown but all are unchecked/greyed out then you have set your filter too high. You will need to click "Enable all Identifications" and the apply filters again, ensuring at least some identifications remain enabled.

Further help is provided in the FAQ.


General Usage