Proteolabels 1.0 User Guide

Experiment Settings

The experiment settings allow you to both manually enter your label information or to allow Proteolabels to auto-detect all settings. Please see the relevant guide sections for further information on each of these features.

Proteolabels supports approaches where chemical or in vivo labels have been introduced onto peptides, giving a fixed mass shift per residue or terminus, and where quantification is performed from MS1 signals (i.e. no current support for MS2 tag approaches). Currently supported styles of labelling experiment are:

  • Duplex "SILAC style": unlabelled "light" channel and heavy labelled
  • Triple "SILAC style": unlabelled "light" channel, medium labelled, heavy labelled
  • Duplex "dimethyl style": light labelled, heavy labelled
  • Triplex "dimethyl style": light labelled, medium labelled, heavy labelled

The styles are indicative of the common types of labelling strategy employed, rather than the actual reagent/labels types. For example, any other chemical or in vivo labelling approaching with a light, medium and heavy label will be detected as "triplex dimethyl style".

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