This familiarization tutorial provides step-by-step instructions for using the Proteome Discoverer application's precursor ion quantification capabilities.

This familiarization exercise uses SILAC-based quantitation. The sample used in this exercise was acquired using Thermo Scientific Orbitrap Elite™ Hybrid Ion Trap-Orbitrap Mass Spectrometer.

For general information about SILAC-based quantitation, go to

Summary of example analysis



Quan method:

SILAC 3plex (Arg6 Lys4, Arg10 Lys8)

Quan channels:

Light, medium, heavy


E. coli


Orbitrap Elite

Acquisition method:

Data dependent MS/MS, HCD

RAW file:


Located in the application media in the folder: Example RAW Files. Copy to a local directory.

Sample Description:

The experiment and labeling approach aimed at 1:2:4 ratios for lysine and 4:2:1 ratios for arginine.

Disk space:

1GB local drive space, SSD drive preferred

Processing time:

Approximately 10 minutes