Hi Sobia,

That is dependent on the accuracy and calibration status of the mass spectrometer you used to analyze the digest.. What machine  did you use?

Thanks!

Having more accurate data, gives higher confidence to your match, as evident by  the MASCOT score. You might get a positive hit for your protein with mass errors of a few hundred ppm, but if your mass spec provides errors of just  a few ppm, your probability of matching the correct protein dramatically increases.

I am attaching my MS profile of my protein sample. Thank you

check out the following for guidance.

https://www.researchgate.net/publication/315874699_Mass_Spectral_Data_Processing

Method Mass Spectral Data Processing

Thank you all.

 Hi Sobia,

If I'm not mistaking what are you doing is peptide mass fingerprint, PMF, using MALDI, for this machine Bruker Ultraflex, I will suggest something between 20-50 ppm, maybe 30 ppm is a good start, and of course the normal parameter for Mascot such as trypsin for the enzyme, 2 miss cleavage, etc

I hope that this is helpful

Yes Sir you are correct. I am doing PMF from Bruker Ultraflex. Around 40 ppm gives the highest score in PMF while for 10 ppm it gives low scores for peptide match. Thank you for the confirmation.