I am analyzing short (13 amino acid long) sythetic peptide by LC-MS. The peptide is not commercially made but produced in a chemistry research lab by a student.
I run ESI-MS (MicroTOF QII Bruker) in positive mode.
After deconvolution of m/z data using maximum entropy algorithm (Bruker's Copmass DataAnalysis software), the resulting monoisotopic mass is one Dalton less then the expected monoisotopic mass, and the isotopic distribution shape does not match the one predicted by IsotopIdent (Expasy) based on the expected peptide sequence.
What could be a reason for the mismatch? Can we conclude that the correct peptide was produced?
Would really appreciate your input! :)