This example of using label-free quantification shows how to find differentiated proteins (E. coli) in a background of undifferentiated proteins (human).

Summary of example analysis

Quan Method


Quan method:

Label free quantification

Data Source:

ProteomeXchange ID: PXD001385


Human, E. coli


Q Exactive Plus

Acquisition method:

Data dependent MS/MS

RAW files:

  • QEP1_SpikeIn_230914_1_3ng_270914.raw
  • QEP1_SpikeIn_230914_2_3ng_270914.raw
  • QEP1_SpikeIn_230914_3_3ng_270914.raw
  • QEP1_SpikeIn_230914_4_7-5ng_270914.raw
  • QEP1_SpikeIn_230914_5_7-5ng_270914.raw
  • QEP1_SpikeIn_230914_6_7-5ng_270914.raw
  • QEP1_SpikeIn_230914_7_10ng_270914.raw
  • QEP1_SpikeIn_230914_8_10ng_270914.raw
  • QEP1_SpikeIn_230914_9_10ng_270914.raw
  • QEP1_SpikeIn_230914_10_15ng_270914.raw
  • QEP1_SpikeIn_230914_11_15ng_270914.raw
  • QEP1_SpikeIn_230914_12_15ng_270914.raw

Sample Description:

Each sample has the same concentration of the human proteome with different amounts of the E. coli proteome spiked into the mixture. Each mix of human and E. coli proteomes has three replicates.

Disk space:

30 GB on local Windows drive, plus 30 GB to store the study; SSD drive preferred

Processing time:

Approximately 6 hours


Use a folder on a local drive that has considerable space. The Proteome Discoverer application stores all .msf and .pdResult files generated for any analyses used for these studies in this folder. Due to the amount of file churn, use an SSD drive if possible. Also, consider using a drive other than the C: drive. Do not use a USB drive.