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Figure 1 | BMC Bioinformatics

Figure 1

From: Statistical methods for quantitative mass spectrometry proteomic experiments with labeling

Figure 1

Cartoon depiction of the 4-plex iTRAQ labeling protocol for one MS experiment. A) Four specimens are each labeled with one of the four tags. The black dots indicate a given peptide that is present in different relative abundance according to size. B) The four specimens are then mixed into a single aliquot for simultaneous MS analysis. The resulting data constitute an MS experiment. C) Each peptide will take some amount of time to elute off of the LC column and so may be observed multiple times. D) In the first MS the top species according to abundance are chosen for a second MS. It is common for the top 3 or 5 to be chosen. E) During the second MS the iTRAQ tags are broken off and used for relative quantification (left in the dotted circle). It is these data that are used in downstream statistical analyses. The remaining peptides are fragmented further for identification purposes (right).

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