[Biojava-l] Biojava MassCalc

[george waldon]

Dear Marc,

The difference is Havg = 1.00794 (see cvs). You calculated the mass MH+ (M plus one ionization H+), which - I guess - is used for mass spectrometry analysis.

Regards,
George

-----Original Message-----
From: Marc Savitsky [mailto:marc at strubi.ox.ac.uk] 
Sent: Wednesday, April 18, 2007 5:41 AM
To: george waldon
Subject: Re: Biojava MassCalc

Hi George,

I had some time to look at the MassCalc.getMolecularWeight(protein) 
method, and it does to job with regard to ambiguous symbols.

Are you aware that it doesn't return the same value as getMass() for 
sequences without ambiguous codes?
My test case examines the sequence

AASLIKPCAYEKQGLIDHAIGSYKVLHDKISESYYKVISRRLERYGIVLDLNGVKEIVKDVVVLHDMGKAGEYYQNQFDDNC
NPLKSNPLKSRFSFIYHELGSALFFYNDYEPINVEKAEEVRSLLTLAVINHLNAIRGISDYLLNRFPDNFDEEMIKLSKYGSILLE
NLRGIISKSLKVRDYSFTDYHDMLYAFSKKSDKYLKLYNLFLAPIMLGDNLDSSLVRNNGSKTRFVGILEGELNGGSTLCCCC

but getMass returns a value of 
28633.94392000000152620486915111541748046875 whereas getMolecularWeight 
returns 28632.9359800000020186416804790496826171875.

regards
Marc Savitsky