Combined in-gel tryptic digestion and CNBr cleavage for the generation of peptide maps of an integral membrane protein with MALDI-TOF mass spectrometry

• Published in: Biochimica et biophysica acta 2002-09, Vol.1555 (1), p.111-115
• Main Authors: van Montfort, Bart A, Doeven, Mark K, Canas, Benito, Veenhoff, Liesbeth M, Poolman, Bert, Robillard, George T
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; CNBr; Cyanogen Bromide; Escherichia coli Proteins; Gels; Hydrophobic and Hydrophilic Interactions; Mass spectrometry; Matrix-assisted laser desorption/ionization; Membrane protein; Membrane Proteins - chemistry; Membrane Transport Proteins - chemistry; Molecular Sequence Data; Monosaccharide Transport Proteins; Peptide mapping; Peptide Mapping - methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Streptococcus - chemistry; Symporters; Trypsin
• ISSN: 0005-2728; 0006-3002; 1879-2650
• DOI: 10.1016/S0005-2728(02)00264-5

A limitation of the in-gel approaches for the generation of peptides of membrane proteins is the size and hydrophobicity of the fragments generated. For membrane proteins like the lactose transporter (LacS) of Streptococcus thermophilus, tryptic digestion or CNBr cleavage yields several hydrophobic fragments larger than 3.5 kDa. As a result, the sequence coverage of the membrane domain is low when the in-gel tryptic-digested or CNBr-cleaved fragments are analyzed by matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS). The combination of tryptic digestion and subsequent CNBr cleavage on the same gel pieces containing LacS approximately doubled the coverage of the hydrophobic membrane domain compared to the individual cleavage methods, while the coverage of the soluble domain remained complete. The fragments formed are predominantly below m/ z 2500, which allows accurate mass measurement.