Matt, 

Alfred Yergey is already on the money with his reply. The apparent addition of water your students mention is probably just the OH+H required to calculate the y ion mass properly by accounting for a full C Terminus AND forming the "new N terminus" at the site of cleavage. Another excellent review by Ioannis Papayannopoulos can be found here: 

http://onlinelibrary.wiley.com/doi/10.1002/mas.1280140104/abstract

Carolina, it is actually the other way around: STED can eliminate an additional water molecule from b or y type ions, you may want to revise your answer.

Best, Christof

Hi matthew, 

This paper may help you: 

Sequence determination of peptides.

Katalin F. Medzihradszky

http://biotech.szbk.u-szeged.hu/docs/MFK_PF_ME_wFigs.doc.

Hi Matt,

y- series ions are from the C-terminal and therefore have a COOH on them. Since they're also protonated, it appears that they have the sum of residue masses + a mole of water. It's just a consequence of being from the C-term.

Al

Mathew, I don't think you can gain a water molecule per se when the peptides are fragmented. If you are using an ammonium salt in your mobile phase, an adduct of NH4+ (+18) might be responsible for the 18 daltons increase.

Amino acids residues as S,T,E,D  gain H2O while R,H,K  lose H2O

http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msproduct

Matt, 

Alfred Yergey is already on the money with his reply. The apparent addition of water your students mention is probably just the OH+H required to calculate the y ion mass properly by accounting for a full C Terminus AND forming the "new N terminus" at the site of cleavage. Another excellent review by Ioannis Papayannopoulos can be found here: 

http://onlinelibrary.wiley.com/doi/10.1002/mas.1280140104/abstract

Carolina, it is actually the other way around: STED can eliminate an additional water molecule from b or y type ions, you may want to revise your answer.

Best, Christof

Hi Matt,

now I'll give my opinion on it. smile

In MS / MS in an ESI-ion trap, in a labile OH group in the molecule (eg in many COOH groups in the molecule), a new molecule in the ion trap are formed. i.e. the parent ion has M / Z = 317 the daughter-ion has M / Z = 335 of [M + H] ION Adding OH and H. OH group comes from the molecule itself and H from a defunct double bond where the OH group binds. While this is quite rare but it does happen, especially in cyclic peptides, or phosphate molecules.

This would be a way !?

Best regards

Burghard Cordes

Yergey and Christof have clearly mentioned that y- ions are the fragment/product ions that possess the -COOH of the parent/precursor ion. I would like to add that the mass of singly charged y- ions are actually calculated as "Sum of the amino acid (a.a) residue masses in the fragment + 19", which is "Sum of the a.a residue masses in the fragment + 18 + 1". This can be rewritten as "Sum of the a.a residue masses in the fragment + 17 + 1 + 1".  17 is due to -OH of the -COOH of the parent/precursor ion. One "1" is due to a "Hydrogen" of the backbone amide group of the precursor ion, about which the fragmentation occurs. Another "1" can be ascribed to a "proton transfer" that could take place from the amide nitrogen of the adjacent a.a residue that precedes the peptide bond, which undergoes dissociation. For a clearer depiction of whatever I have described above, kindly have a look at the following articles: 

1. Biemann K. Methods Enzymol. (1990) Vol.193, p.455-479.

2. Schlosser A. & Lehmann WD. J. Mass Spectrom. (2000) Vol.35, p.1382-1390.

3. Summerfield SG, Bolgar MS & Gaskell SJ. J. Mass Spectrom. (1997) Vol.32, 225-231.

If you are not able to get .pdf of the above articles, I will try to send you any one or two of these.

sabareesh.