THRESOLD FOR ASSIGNED MSi scores

[Sandeep Kumar Bansal]

Dear Siri,

I had a list of peptides which I used for peptide-allele prediction. I got assigned MSi scores for some of those peptides ranging from 0.1 to 0.99. What score can I consider as a threshold that a peptide is definitely presented by that allele.

Please reply.

Thank you!

Regards,

Sandeep Kumar Bansal

UTHealth Science Center Houston

[Sisi Sarkizova]

Hi Sandeep, the MSi scores are the predicted likelihoods of binding so you can think of them as probabilities (1 is good, 0 is bad). I'd consider these scores as a continuous distribution rather than a strict threshold but as a general guidance I'd say scores >0.85 would tend to be high confidence binders. Please note that the algorithm also outputs percentile ranks (similarly to other prediction tools).

Best,

Sisi

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[Sandeep Kumar Bansal]

Dear Sir,

Thank you for your response. It means a lot to me. I appreciate it. I have one more query. In percentile rank output, could you please suggest any cut off score for high confidence binders with your experience?

Regards,

Sandeep Kumar Bansal