Parent ion mass

[Thys Potgieter]

Hi Guys! Please excuse any ignorance in this question. From the blast_output.txt file, I am trying to get the precursor ion molecular weight.

Can I get this from the fasta header below? I think mz x charge like this: 896.964247854659 x 2 = 1793.928495709318 MW

Thank you in advance!

Thys

 

>150715_SF_507_ST(2).mgf;150715_SF_507_ST(2).43782.43782.2 File:"150715_SF_507_ST(2).raw", NativeID:"controllerType=0 controllerNumber=1 scan=43782";896.964247854659;2+;-3.739;88.729

AVTSLAGEYAELGR

[Harald Barsnes]

Hi Thys,

You are right that "896.964247854659" is the m/z value and that "2+" is the charge, and your calculation is almost right. You are however forgetting to remove the protons.

Given that:

m/z = (peptide mass + (proton mass x number of protons)) / (number of protons)

To get the peptide mass from the m/z value you therefore have to do:

peptide mass = (m/z * (number of protons)) - (proton mass x number of protons)

However, note that the BLAST output does not contain information about PTMs (as this cannot be considered in the BLAST algorithm), hence the conversion will not be correct if the peptide is modified (or if it contains terminal gaps as for the tag algorithms). Your example above seems indicate that this specific peptide is modified? Otherwise I cannot get the numbers to work.

Best regards,

Harald

[Thys Potgieter]

Thank you Harald, that is very helpful. I can't confirm that the peptide is modified as I dont have the tag export table on hand, only the BLAST file (but im sure it is!). Does the BLAST export also include tag sequences, excluding the regions of uncertainty on the terminals? This may be another reason for apparent discrepancies? I will see if I can export the tag table to check.

Thank you!

[Harald Barsnes]

Hi Thys,

> Does the BLAST export also include tag sequences, excluding the regions of uncertainty on the terminals? This may be another reason for apparent discrepancies?

Yes, tag sequences are also included in the BLAST export. Which is what I tried to refer to in my original email with "or if it contains terminal gaps as for the tag algorithms". :)

Best regards,

Harald