Data processing

What you will get

Depending on analytical workflow, results will be provided in different formats:

WorkflowResultsTutorial
Protein identification
(by Mascot)		– Scaffold file (.sf3)
– Excel table		Shotgun analysis
Targeted protein quantification
(Simple Western)		– Excel table
– Report		Western capillary
Protein quantification
(labeled or label-free)		– Excel table (with statistics)
– Report		Quantitative analysis
Phosphorylation quantification
(combined with TMT)		– Excel table (with statistics)
– Report		Phosphoproteomics analysis
For proteomics quantitative experiments, you receive a table with a list of proteins (or modification sites in case of PTM’s) and columns with associated quantitative values. Some statistical tests to compare conditions are performed and a basic pathway enrichment analysis is included.

Publication

  • Specific material and methods for proteomics analyses are available on demand.
    Sample ID numbers must be provided in your request.
  • Most journals ask for data submission to a repository before article publication. For now, our facility takes care of data submission to ProteomeXchange repository. Please follow the instructions provided in this tutorial.
  • Regarding PAF acknowledgements or eventual co-authorship, please refer to our policy and publication guidelines.