I'm purifying a protein using bacterial expression system. Purification is done using affinity chromatography. While on the SDS PAGE it shows band at expected mass (17 kDa) but molecular mass obtained through mass spectroscopy is higher by 1kDa (18 kDa) using the Sinapic acid as matrix. Other protein with same molecular weight are giving exact mass in Mass spectroscopy.
As already noted, you need to provide more information before we can attempt to troubleshoot your problem. How big is the protein? What kind of MS? What matrix are you using?
SDS accuracy could be the problem. It could also be due to extraction methods or the matrix itself causing breakages in the protein. Have you checked the lower masses for a peptide(s) roughly that mass change?
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