identification by mass spectrometry branch cleanup

[lukasz99]

This is mostly to make the terms more generic by decoupling MS methods from any specific molecule type and by decoupling mudpit from any specific chromatography and/or any specific MS/MS technology. Proposed changes:

MI:0032 (de novo protein sequencing by mass spectrometry) will be changed into 'tandem MS/MS' defined as:
Tandem MS/MS spectroscopy identify molecules by analyzing fragmentation spectra
of the initial MS peaks. It is commonly used to determine the amino acid sequence
of proteins where it relies on the generation, within MS/MS instrument, of
a nested set of fragments differing by one amino acid. Here, the fragmentation spectra
reveal the identity of the residues that have been removed at each degradation step
by measuring the mass difference of fragments differing of one residue. Tandem MS/MS
analysis is often performed on a set of peptides generated by protease treatment
of the protein (or mixture of proteins) of interest.

COMMENT: the change makes the term molecule type and MS technology neutral. It still applies
to de novo sequencing which is just a special case of tandem MS/MS as applied to proteins.

MI:0082 (peptide mass fingerprinting) definition will be simplified to read:
Protein identification by matching peptide masses, as measured by mass spectrometry,
to the ones calculated by applying in silico proteolityc fragmentation of the candidate protein
retrieved form a sequence database.

COMMENT: The change removes the way too long essay that currently hides as definition.

MI:0658 (multidimensional protein identification technology) will be simplified to read:
MudPIT is a method for rapid and large-scale protein identification by liquid
chromatography of protein fragments, which are typically generated by protease treatment,
that is followed by a tandem MS/MS mass spectrometry.

Apart from the definition change, MI:0658 has to be removed from predetermined branch as it can be (and typically is) used to identify arbitrary proteins

COMMENT: This makes mudpit generalized to any type of LC followed by tandem MS/MS step.

[lukasz99]

Alternative to making MI:0032 into a generic 'tandem MS/MS' is to add a new, generic tandem MS/MS term and then make MI:0032 its child. I'm not sure, though, if it is worth the trouble...