[TheUnassuming]

Something my friend has suggested is contamination from PEG leaching.
When I remove the completed peptide from the synthesizer, I do the final deprotection and acetylation in a plastic frit (ones used for automated columns;empty of silica of course), and I do my cleavages in PCR tubes. Could this be a potential source?

Possible, but most likely not as I've seen and done much the same myself for other substrates. Usually for me, when you start to break down the plastics you get a mess of phthalates.   

[kriggy]

Probably not, because Na adds 23 so two sodium atoms are +46 and even than, it would change the ratio of M/z because you then have 2 charges on the molecule

Not quite----2 x H are replaced, so +44.

Also, (RCOO-Na+)Na+ is singly charged, as is AspCOONaGluCOONa)H+

Oh you are right, I totaly forgot about the protons, thanks for clarification.

[MOTOBALL]

You need high resolution accurate mass MS on both the expected product & the +44 amu.  The difference will let you determine the composition of the unknown.

Regards.

[vitaminvater]

So after talking with colleagues who had worked with the same sequence in the past, it seems the M+44 masses are peptides that have not been fully deprotected. After leaving the cleaved peptide agitating in a 1:1 solution of MeCN:H2O (+0.1% TFA) for 24 hrs, the M+44 peaks had practically disappeared (confirmed by HPLC and UPLC).

Thanks for all the *delete me* I think after purifying my peptides I'll send it off for AA analysis to determine which AA had the troublesome PG.