Mass spectrometer protein identification

Figeys, D., Lock, C., Taylor, L., and Aebersold, R. (1998). Microfabricated device coupled with an electrospray ionization quadrupole time-of-flight mass spectrometer protein identifications based on enhanced-resolution mass spectrometry and tandem mass spectrometry data. Rapid Commun. Mass Spectrom. 12, 1435 — 1444. 

Gharahdaghi F, et al (1999) Mass spectromet-ric identification of proteins firom silver-stained polyacrylamide gel A method for the removal... 

Figeys, D. Aebersold, R. High sensitivity identification of proteins by electrospray ionization tandem mass spectrometry inital comparison between an ion trap mass spectrometer and a triple quadrupole mass spectrometer. Electrophoresis 1997,18, 360-368. 

Multiply charged proteins can also be partially sequenced, and microsequences of proteins isolated from several microorganisms have been reported, accomplished with electrospray ionization and FTMS.23,90 Nonadjacent fragment ions may be used to identify bacterial proteins in these top-down strategies.91 In all cases these sequences could be related by bioinformatics to the parent species. An obvious extension would be to characterize proteins from intact microorganisms in this way. In at least one instance a microsequence has been obtained from a protein released from a contaminated intact bacteriophage sample (MS2) to provide a chemotaxonomic identification.77 This work was carried out in an ion trap mass spectrometer. 

There exist essentially three categories of SCX/RP/MS/MS approaches. In one approach, SCX is run off-line followed by on-line RP/MS/MS (Fig. 11.1). In the offline SCX approach, fractions do not directly elute onto RP material but rather are collected. In one of the two in-line approaches, SCX is run in line with RP/MS/MS using different columns for SCX and RP (Fig. 11.2). In the multidimensional protein identification technology approach (MudPIT), SCX and RP are run in line in the same column, and this column serves as the ion source for a tandem mass spectrometer (Fig. 11.3). Both the in-line approaches are true SCX/RP/MS/MS approaches the first approach could be abbreviated as SCX—RP/MS/MS where... 

Fig. 6. Protein identification using a peptide map measured with a matrix-assisted laser desorption time-of-flight mass spectrometer. All the peptide extracted from the gel is measured and the set of masses is used in the database search. The mass resolution is in the order of 10,000. Individual isotopes of a 2.5 kDa peptide are clearly resolved.

Fig. 7. Protein identification with electrospray tandem mass spectrometry and a triple quadrupole mass spectrometer. Fragment spectra of several peptides are generated during one investigation. From the fragment spectra short sequence stretches can be read. Together with their mass location in the peptide of the measured mass, they can be used to specifically identify a protein in the database. Because the protein identification depends only on one peptide, several proteins can be identified from one sample.

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