- General Usage
In most cases Proteolabels is able to auto-detect the most optimal settings for your project. If for some reason Proteolabels failed to auto-detect any settings or gets the settings wrong then please see the FAQ entry on "Why has auto-detect failed?" for common reasons and solutions.
Auto-detect will automatically detect the settings for both duplex and triplex runs where their is sufficient identification data. On first loading a project the auto-detect process should automatically initiate. If you need to execute auto-detect again due you can do so by clicking the "auto-detect" button on the left hand side.
Auto-detect will select conservative tolerance values to increase data quality. Increasing these values will increase the number of results found, however, this may result in an increased number of false positives peptide pairs/triples. It is advised not to alter these values unless necessary, for example if the labelling strategy you have employed has unpredictable effects on retention time.