Elastase digests: new ammunition for shotgun membrane proteomics.
Despite many advances in membrane proteomics during the last decade the fundamental problem of accessing the transmembrane regions itself has only been addressed to some extent. The present study establishes a method for the nano-LC-based analysis of complex membrane proteomes on the basis of a methanolic porcine pancreatic elastase digest to increase transmembrane coverage. Halobacterium salinarium purple and Corynebacterium glutamicum membranes were successfully analyzed by using the new protocol. We demonstrated that elastase digests yield a large proportion of transmembrane peptides, facilitating membrane protein identification. The potential for characterization of a membrane protein through full sequence coverage using elastase is there but is restricted to the higher abundance protein components. Compatibility of the work flow with the two most common mass spectrometric ionization techniques, ESI and MALDI, was shown. Currently better results are obtained using ESI mainly because of the low response of MALDI for strictly neutral peptides. New findings concerning elastase specificity in complex protein mixtures reveal a new prospect beyond the application in shotgun experiments. Furthermore peptide mass fingerprinting with less specific enzymes might be done in the near future but requires an adaptation of current search algorithms to the new proteases.
Rietschel
Benjamin
B
Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438, Frankfurt, Germany.
Arrey
Tabiwang N
TN
Meyer
Bjoern
B
Bornemann
Sandra
S
Schuerken
Malte
M
Karas
Michael
M
Poetsch
Ansgar
A
D000595:Amino Acid Sequence; D000818:Animals; D001436:Bacteriorhodopsins / Q000737:chemistry; D048230:Corynebacterium glutamicum / Q000378:metabolism; D019617:Halobacterium salinarum / Q000378:metabolism; D007526:Isoelectric Point; D008565:Membrane Proteins / Q000032:analysis*; D008969:Molecular Sequence Data; D010196:Pancreatic Elastase / Q000378:metabolism*; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D018717:Purple Membrane / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D034421:Sus scrofa
D008565:Membrane Proteins; D010455:Peptides; D001436:Bacteriorhodopsins; D010196:Pancreatic Elastase