do you get consistent results on MALDI? - peptide mass fingerprinting? (Jul/20/2008 )

Hi,

I am working on 4800 MALDI TOF TOF. Normally as we do, I cut the protein bands from coomassie stained gels and after in gel trypsinization, I spot the samples on MALDI plate for PMF. My problem is i don't get consistent results. If once I've got 70% true positive hits , next time it doesn't work for the same samples . I know it depends on spoting and matrix. but for spoting i don't believe because i do it everytime in the same manner.And about matrix, I've made the stock solution and kept it at 4 degree. everytime I just make the working from it and use it. Has anyone faced the same problem? Do you everytime make fresh matrix? I don't know what to do to get the consistency in this, Anyone please help me, its very frustating that once you get results and other time you don't get it

Are you doing everything in automatic mode? MALDI crystals are not always homogenous, so if you hit hot spots, you get very good spectra. If you do automatic, chances are you may not always hit hotspots and so results could vary. Manually, you can make sure you only acquire and accumulate spectra if they are good.

Matrix stock (CHCA) is ok to keep at 4C as far as I know.