We have done LC/MS-MS analysis and executed Proteome Discoverer for identification of proteins. In the output, I found there are many proteins fragments and also found that one protein present more than two times with different Uniprot accession and also with different PSMs.
1. How do I interpret protein fragments, should I consider as the whole protein and consider for analysis?
2. why there are duplication of proteins with different accessions and different PSM. How do I interpret ?
Hi Monica Steffi Matchado ,
Please take the protein groups into consideration instead of taking proteins table. The proteins in a group are ranked according to the number of peptide sequences, the number of PSMs, their protein scores, and the sequence coverage. The top-ranking protein of a group becomes the master protein of that group.
Thank you.
Hi Varshasnata Mohanty
Thank you for your reply. It gave me a clear idea.
Just for clarification, even for protein fragments, I should go with protein groups right?
Hi Monica Steffi Matchado ,
If you are referring protein fragments as peptides, then you should consider peptide groups tables for getting the concise list of peptides obtained from your result.
Thank you.
Dear Varshasnata Mohanty
For example, i got one entry as
Accession Protein_Name PSM
B1Q387 Ferritin (Fragment) 224
How do I infer this protein. Can I consider as a valid protein entry
As you have got such a high PSM count of your protein, it is a valid protein and you can consider. Additionally, you can check the spectra of the peptide belonging to this protein.
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