#239 MzIdentMLWriter and Reader Calculated Mass To Charge Value Incorrect

[Alice Cheng]

MzIdentMLWriter.cpp is using following formula to write calculated mass to charge:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass()+MASS_PROTON)/(double)zstate.getCharge());

Suggested Fix:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass() + ((FLOAT_T)zstate.getCharge() * MASS_PROTON)) / ((FLOAT_T)zstate.getCharge()));

MzIdentMLReader.cpp is using following formula to set peptide neutral mass.

FLOAT_T calc_mass = (calc_mz - MASS_PROTON ) * (FLOAT_T)charge;

Suggested Fix:

FLOAT_T calc_mass = (calc_mz * (FLOAT_T)charge) - ((FLOAT_T)charge * MASS_PROTON);

[Jeff Howbert]

Hi ALice,

Your proposed fix for the first formula looks correct. Please implement.

The second formula (peptide neutral mass) is already correct. Your suggested fix is just a rearrangement of terms and is unnecessary.

Best,

Jeff

On Tue, 3 Feb 2015, Alice Cheng wrote:

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** [issues:#239] MzIdentMLWriter and Reader Calculated Mass To Charge Value Incorrect**

Status: open
Milestone: post v2.0
Created: Tue Feb 03, 2015 11:39 PM UTC by Alice Cheng
Last Updated: Tue Feb 03, 2015 11:39 PM UTC
Owner: nobody

MzIdentMLWriter.cpp is using following formula to write calculated mass to charge:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass()+MASS_PROTON)/(double)zstate.getCharge());

Suggested Fix:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass() + ((FLOAT_T)zstate.getCharge() * MASS_PROTON)) / ((FLOAT_T)zstate.getCharge()));

MzIdentMLReader.cpp is using following formula to set peptide neutral mass.

FLOAT_T calc_mass = (calc_mz - MASS_PROTON ) * (FLOAT_T)charge;

Suggested Fix:

FLOAT_T calc_mass = (calc_mz * (FLOAT_T)charge) - ((FLOAT_T)charge * MASS_PROTON);

---

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[sjoemac]

Jeff, Alice,

Maybe we should use/write a macro or inline function for this if it already doesn't exist in crux.

Thanks,
Sean

On Feb 3, 2015, at 6:32 PM, Jeff Howbert howbert@users.sf.net wrote:

Hi ALice,

Your proposed fix for the first formula looks correct. Please implement.

The second formula (peptide neutral mass) is already correct. Your suggested fix is just a rearrangement of terms and is unnecessary.

Best,

Jeff

On Tue, 3 Feb 2015, Alice Cheng wrote:

---

** [issues:#239] MzIdentMLWriter and Reader Calculated Mass To Charge Value Incorrect**

Status: open
Milestone: post v2.0
Created: Tue Feb 03, 2015 11:39 PM UTC by Alice Cheng
Last Updated: Tue Feb 03, 2015 11:39 PM UTC
Owner: nobody

MzIdentMLWriter.cpp is using following formula to write calculated mass to charge:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass()+MASS_PROTON)/(double)zstate.getCharge());

Suggested Fix:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass() + ((FLOAT_T)zstate.getCharge() * MASS_PROTON)) / ((FLOAT_T)zstate.getCharge()));

MzIdentMLReader.cpp is using following formula to set peptide neutral mass.

FLOAT_T calc_mass = (calc_mz - MASS_PROTON ) * (FLOAT_T)charge;

Suggested Fix:

FLOAT_T calc_mass = (calc_mz * (FLOAT_T)charge) - ((FLOAT_T)charge * MASS_PROTON);

---

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cruxtoolkit/issues/239/

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---

** [issues:#239] MzIdentMLWriter and Reader Calculated Mass To Charge Value Incorrect**

Status: open
Milestone: post v2.0
Created: Tue Feb 03, 2015 11:39 PM UTC by Alice Cheng
Last Updated: Tue Feb 03, 2015 11:39 PM UTC
Owner: nobody

MzIdentMLWriter.cpp is using following formula to write calculated mass to charge:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass()+MASS_PROTON)/(double)zstate.getCharge());

Suggested Fix:

siip->calculatedMassToCharge = FLOAT_T((peptide->getPeptideMass() + ((FLOAT_T)zstate.getCharge() * MASS_PROTON)) / ((FLOAT_T)zstate.getCharge()));

MzIdentMLReader.cpp is using following formula to set peptide neutral mass.

FLOAT_T calc_mass = (calc_mz - MASS_PROTON ) * (FLOAT_T)charge;

Suggested Fix:

FLOAT_T calc_mass = (calc_mz * (FLOAT_T)charge) - ((FLOAT_T)charge * MASS_PROTON);

---

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