[ahayes]

I don't think you understand how this protein sequencing was done. Here is a page that may help describe it. They started with sad scraps of protein and reduced them to even smaller scraps before feeding them into the mass spec. Having a large number of partial fragments of the protein allows them to determine most of the protein sequence. This isn't a linear method like sequencing short DNAs or Edman degradation of peptides. It's more like the nonlinear method for sequencing the human genome--sequencing overlapping segments and then putting it all together.

[Sola Veritas]

I’ve worked extensively with both Gas Chromatographs and Mass Spectrometers. Although, I am not saying the method you mention is unreliable to the point it negates the findings, they themselves post some interesting conclusions:

“The use of MALDI spectrometry alone is rarely sufficient to identify a protein. If the protein is not mixed, and gives rise to several peptides, and several of these give matches against the same protein in a good complete library for the species, it may be possible to obtain an identification. More often, MALDI spectrometry cannot prove what protein was present, but can provide a list of likely candidates. This is useful, as then the peptides that provide evidence for these candidate proteins can be taken forward for MS/MS spectrometry, which is more likely to provide convincing proof of protein identity.”