Black,

Please, find the answer of your question regarding [M+H]+ and [M-H]- spectrometry modes in the following

---http://masspec.scripps.edu/publications/public_pdf/78_art.pdf

Good luck

After you read Gary's paper linked by Adel Amer, here's a nice little - and useful - set of utilities: http://db.systemsbiology.net:8080/proteomicsToolkit/

If you type a peptide sequence into the MS/MS Fragment calculator, it will give you the MH+ value for the peptide along with those for the various CID fragments. And you can even add modifications.

The easiest explanation can be found at

http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm

Following is the relevant text from the the above mentioned article.

Positive or negative ionisation?

If the sample has functional groups that readily accept a proton (H+) then positive ion detection is used

e.g. amines R-NH2 + H+ = R-NH3+ as in proteins or peptides.

If the sample has functional groups that readily lose a proton then negative ion detection is used

e.g. carboxylic acids R-CO2H = R-CO2- and alcohols R-OH = R-O- as in saccharides or oligonucleotides