delta mass calculation for percolator .pin file

[Dennis Goldfarb]

Hey Jimmy,

It looks like the dM calculation in CometWritePercolator is using the mass of the top candidate her spectrum instead of the mass of the specific candidate. For example the pin file looks like this currently:

ScanNr, ExpMass, CalcMass, dM

7, 1243.635302, 1241.631335, 0.001614

7, 1243.635302, 1240.606432, 0.001614

7, 1243.635302, 1243.652835, 0.001614

7, 1243.635302, 1243.638944, 0.001614

7, 1243.635302, 1242.646376, 0.001614

line #280 of CometWritePercolator is:

double dMassDiff = (pQuery->_pepMassInfo.dExpPepMass - pOutput[0].dPepMass) / pOutput[0].dPepMass;

but I believe it should be:

double dMassDiff = (pQuery->_pepMassInfo.dExpPepMass - pOutput[iWhichResult].dPepMass) / pOutput[iWhichResult].dPepMass;

With the updated code, the pin file becomes:

ScanNr, ExpMass, CalcMass, dM

7, 1243.635302, 1241.631335, 0.001614

7, 1243.635302, 1240.606432, 0.002441

7, 1243.635302, 1243.652835, -0.000014

7, 1243.635302, 1243.638944, -0.000003

7, 1243.635302, 1242.646376, 0.000796

I used comet (2020.01 rev. 3) + percolator (v3.04.0) on one of our HeLa standards +- the dMassDiff correction.

Original: 10617 PSMs and 7372 peptides with q<0.01

New: 11000 PSMs and 7807 peptides with q<0.01

Hope this helps.

Best, 

Dennis

[Jimmy Eng]

Dennis, thank you for identifying the bug.  I'll include the fix in the next release.

[Manuel Belmadani]

Hi Jimmy and Dennis,

Would this affect only the .pin output files or if other output formats are also affected? 

Thank you,

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[Jimmy Eng]

Only the .pin output.