Hi,
I dont understand if having same protein id will affect the result. I see no
point in reporting a peptide twice if the protein remains the same.
The problem broken down is -
- same spectra with 2 diff charge states is generally searched once as 2+
precursor and second time as 3+ (so they r now 2 spectra)
- Both cannot (in any case) match the same peptide because deconvoluting
to 2+ and 3+ will change the precursor mass and they cannot be in each
other's vicinity then.
- OMSSA is returning same peptide for diff charge states (deconvoluted
masses are reported to be the same).
- I took one such case from OMSSA result -
- 1568 QT20060328_Den18mix_07.03255.03255.2VPTPNVSVVDLTCR 3.32E-10
1555.74 0 11 233 246 sp|P46406|G3P_RABIT GLYCERALDEHYDE 3-PHOSPHATE
DEHYDROGENASE (EC 1.2.1.12) (GAPDH) - Oryctolagus cuniculus (Rabbit). 2
1556.79 1.62E-12 0 1569 QT20060328_Den18mix_07.03255.03255.3
VPTPNVSVVDLTCR
3.32E-10 1555.74 0 11 233 246 sp|P46406|G3P_RABIT GLYCERALDEHYDE
3-PHOSPHATE
DEHYDROGENASE (EC 1.2.1.12) (GAPDH) - Oryctolagus cuniculus (Rabbit). 2
1556.79 1.62E-12 0
Here are the first few lines of two spectra with charge 2 and 3(mapped to
mgf using spectra id of omssa result)
(1)
BEGIN IONS
PEPMASS=778.879883 1.0000
CHARGE=2+
TITLE=QT20060328_Den18mix_07.03255.03255.2
154.089462 3.037975
155.064362 3.037975.......
(2)
BEGIN IONS
PEPMASS=778.879883 1.0000
CHARGE=3+
TITLE=QT20060328_Den18mix_07.03255.03255.3
154.089462 3.037975
155.064362 3.037975......
Regards,
Amit Kumar Yadav
Senior Research Fellow (SRF-CSIR)
IGIB, New Delhi (India)
http://masswiz.igib.res.in
On Tue, Jun 8, 2010 at 4:14 AM, Jesse J <[email protected]> wrote:
> You say that these duplicate peptides have the same score values, but
> do they have the same protein ID/description?
>
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