We were operating somewhat blindly in identifying proteins using MALDI-TOF MS, but there are tools out there that will enable you identify a protein based on its trypsin-digested peptide profile. I mostly used ExPASy's proteomics tools for manual identification. Maybe my publication would be useful...

Article Mass Spectrometric Analysis of the N Terminus of Translation...

 It is a good discussion point about the meaning of identification. It also depends on what type of sample you are talking about. Is it a naturally occuring protein and its sequence is already in the protein database? In case of a recombinant protein that you expressed and purified, all bets are off as only you know the putative sequence.

After measuring the MW of the protein by any mass spectrometric method, what are you going to compare the result with?

In general, a good match between a theoretical MW based on a putative sequence and experimentally measured MW from your sample is a necessary, but not a sufficient condition to 'identify' the specific protein. 

Are you talking about top-down mass spectrometry (undigested proteins)?

thank you Christopher Bradley, you paper was really helpful. in case of sds page band,  Molecular weight obtained from  ESI MS spectrum, would be helpful to identify the protein compare with putative sequence from database ?

Thank you Viswanatham Katta, basically i want to compare a diseased condition with an normal condition after determination of MW via ESI MS analysis. would it be possible ?

dear Daniel Lorenz Winter, basically i am trying to compare the diseased condition with normal condition. in case of obtaining MW from ESI MS, would it be possible to identify the protein from its MW ? basically i am going with bottom up approaches.

A big challenge with identifying a protein solely on the basis of its molecular weight, even given the masses of all the proteins in the proteome, is that proteins are frequently post-translationally modified. As a result, the measured mass does not equal the predicted mass based on the amino acid sequence. In contrast, a few sequenced residues would be enough to identify the protein.

Well, then the question is taking a different shape. Let us stick to the case of 'normal' condition. Does the MW of the protein you measured in the 'normal' state match with the predicted based on the amino acid sequence? As Adam Shapiro mentioned there could be many modifications that need to be accounted for. Are you isolating this protein from a complex mixture? Are there any steps, such as the affinity chromatography, that will provide additional benefit to say that you are looking at the specific protein?