Data processing – Protein Analysis Facility

What you will get

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

*Workflow*	*Results*	*Tutorial*
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.