Lost of Reproducibility - (Sep/09/2012 )

I have recently started working on LC/MS. I tested my standard compound PGA2 and got a peak of m/z ratio of 325. This peak was reproduced once but when I ran the same standard solution 2 more times the peak disappeared. The run showed same results as the run for water. Can any one tell me why my peak disappeared when I haven't changed any parameters.

Protease contamination of the sample?

There is nothing that I have mixed with the sample. The sample is in the vial as made and I had stored the sample in -20C

Aggregation of the sample, damage to the protein with freeze/thaw...

I am not analyzing protein but using Postaglandin 2. Since I was getting this problem I called up the supplier and they told me that the solvent I dissolved the PGE2 in (acetonitrile) might have caused them to degrade because of change in pH.
But I m still confused as if the sample has degraded the degraded substance should have show a peak in the chromatogram which was not seen.