ASPECTS OF OLIGONUCLEOTIDE AND PEPTIDE SEQUENCING WITH MALDI AND ELECTROSPRAY MASS-SPECTROMETRY

Biopolymer sequencing with mass spectrometry has become increasingly i mportant and accessible with the development of matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). Here we examine the use of sequential digestion for the rapid identificatio n of proteolytic fragments, in turn highlighting the general utility o f enzymatic MALDI ladder sequencing and ESI tandem mass spectrometry. Analyses were performed on oligonucleotides ranging in size from 2 to 50 residues, on peptides ranging in size from 7 to 44 residues and on viral coat proteins. MALDI ladder sequencing using exonuclease digesti on generated a uniform distribution of ions and provided complete sequ ence information on the oligonucleotides 2-30 nucleic acid residues lo ng. Only partial sequence information was obtained on the longer oligo nucleotides. C-terminal peptide ladder sequencing typically provided i nformation from 4 to 7 amino acids into the peptide. Sequential digest ion, or endoprotease followed by exoprotease exposure, was also succes sfully applied to a trypsin digest of viral proteins. Analysis of ladd er sequenced peptides by LCMS generated less information than in the M ALDI-MS analysis and ESI-MS2 normally provided partial sequence inform ation on both the small oligonucleotides and peptides. In general, MAL DI ladder sequencing offered information on a broader mass range of bi opolymers than ESI-MS2 and was relatively straightforward to interpret , especially for oligonucleotides. (C) 1998 Elsevier Science Ltd. All rights reserved.