In-House scripts for proteomic analysis

Frequently Asked Questions

1) Where can I get the Human/Mouse databases?
You can download the databases of Human and Mouse here (To save, "right click" and opt for "save link as").

2) My experiments is based on Xenograft. Can these scripts fetch phosphosites from combined database of Human and Mouse?
No, currently the scripts are not meant for xenograft studies. We will implement this option in the future.

3) I don't have protein group accession, instead I have Gene symbol/NP_accession/gene_id. Can I get the list of protein group accession?
Yes, you can convert the query accession to fetch protein group accession. The scripts will be integrated in the InHouse scripts "GI converter" soon.

4) I don't have protein group accession. Can I still fetch the sites?
Yes. You can perform a string search of your peptides to the database and get the protein group accession. The ideal situation is to get these accession by the proteome discoverer searches.

5) Is their any option to use customized database searches?
We are implementing this option in future. However you can request to include your custome database by writing to tech at ibioinformatics dot org.

6) I don't have PhosphoRS probabilities. Can I still fetch the sites?
No. You should have the PhosphoRS probabilities.

7) Are you planning to include a similar analysis pipeline for other post translational modifications (PTMs)
Yes. We will soon include the InHouse scripts for other PTMs as well.

If you have a specific question, feedback or would like to contribute to developing a customized tool in the InHouse scripts, please write to arun at ibioinformatics dot org -or- tech at ibioinformatics dot org. Please include "InHouse: FAQ" in the subject line.