小中大Sorry I can not type in Chinese.
If 一维电泳 is SDS PAGE, one spot may contain multiple components. No matter what, the molecular weight of the protein from SDS PAGE reflects the real molecular weight of the protein except the protein is dissociated during denature or electrophoresis. The molecular weight of protein in database is the theoretical molecular weight predicted from sequence, where the signal peptide removal or various modification is not considered until it is reported by some paper. Thus the molecular weight is a very important parameter to Verify the modifications. For example, the theoretical MW of insulin or bovine serum albumin in database is more than their experimental MW due to signal peptide removal.
I think the result you get is very interesting. If database match gives very good score, one of the proteins may contain this fragment, but definitely, the protein given is not the protein you are looking for since such huge discrepancy on molecular weight, especially the theoretical MW much less than experimental MW. You could do a FASTA or BLAST homology search to see if there is any other proteins contain this peptide. However, this only can give you some clue, not the final answer.
There are several ways to verify:
1. get better separation of proteins using 2D gel or affinity(maybe more specific since you are looking for antibody, assuming you already know the antibody)
2. multiple peptides fragmentation in MS/MS to improve match, or using instruments with better mass accuracy.
If you could find proteins with multiple modifications, it will be more interesting. Anyway, good luck.
