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FAQs - Interaction Proteomics
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Yes, we offer on-beads digestion!
[+] Can we bring samples at any time?
It is always better to synchronize with FGCZ before bringing your samples.
NOTE: bead-bound samples that require "same day processing" must be delivered Monday to Thursday till 15:00!
[+] Do you support Proximity Labeling experiment?
[+] Do you always request a preliminary pilot test, prior to any interaction proteomics experiment?
No, but we encourage to go through a pilot experiment to make sure that tools, affinity reagents, protocol are delivering optimal performance.
[+] Do you know any software that could be used for the evaluation of the affinity proteomics (AP-MS) experiments?
New tools are always appearing for the evaluation of AP-MS experiments. All our experiments will be processed using SAINT (see below). If you want to proceed on your own, we suggest the following ones:
- REPRINT: Resource for Evaluation of Protein Interaction Networks
- Cytoscape: Network Data Integration, Analysis, and Visualization in a Box
- String: Protein-Protein interaction networks
[+] What will FGCZ provide as a result of the experiment?
For protein-protein interaction experiments the results normally consist of:
- Intensity-based quantification (MS1- or MS2-level)
- such workflows are usually our first choice for interaction proteomics experiments.
- Protein identification and quantification using FragPipe (MS1-level) or DIA-NN (MS2-level)
- Data analysis using Significance Analysis of INTeractome (SAINT) express
- Pdf Report with information on the used protocol and comment on the results
- Spectral counts:
- Data analysis using Significance Analysis of INTeractome (SAINT) express
- Reports, tables, and plots
- Scaffold file with all the results obtained using the FragPipe MS-Fragger search engine.
- Pdf Report with information on the used protocol and comment on the results
- the results obtained using alternative search engines (e.g. PEAKS, Byonic, Mascot,...) are provided when needed (e.g., when customized databases are used)
[+] How can I change some settings in Scaffold?
Please have a look at the following resources
- Scaffold: Scaffold files (Proteome Software) can be used for the visualization of the protein and peptide identification results. Scaffold can be downloaded here: without a license, it woks as a Free Viewer.