Membrane protein identification: N-terminal labeling of nontryptic membrane protein peptides facilitates database searching.
Membrane proteins are fairly refractory to digestion especially by trypsin, and less specific proteases, such as elastase and pepsin, are much more effective. However, database searching using nontryptic peptides is much less effective because of the lack of charge localization at the N and C termini and the absence of sequence specificity. We describe a method for N-terminal-specific labeling of peptides from nontryptic digestions of membrane proteins, which facilitates Mascot database searching and can be used for relative quantitation. The conditions for digestion have been optimized to obtain peptides of a suitable length for mass spectrometry (MS) fragmentation. We show the effectiveness of the method using a plasma membrane preparation from a leukemia cell line and demonstrate a large increase in the number of membrane proteins, with small extra-membranar domains being identified in comparison to previous published methods.
Jansson
Maria
M
Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden.
Wårell
Kristofer
K
Levander
Fredrik
F
James
Peter
P
D000595:Amino Acid Sequence; D030562:Databases, Protein; D004591:Electrophoresis, Polyacrylamide Gel; D019286:Endopeptidase K; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D010434:Pepsin A; D010446:Peptide Fragments / Q000737:chemistry* / Q000302:isolation & purification; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013194:Staining and Labeling; D053719:Tandem Mass Spectrometry; D020298:U937 Cells
D008565:Membrane Proteins; D010446:Peptide Fragments; D019286:Endopeptidase K; D010434:Pepsin A