De novo sequencing of peptides using MALDI/TOF-TOF.
The recently developed MALDI TOF-TOF instrument yields relatively complex but interpretable fragmentation spectra. When coupled with a straightforward sequence extension algorithm, it is possible to develop complete peptide sequences de novo from the spectra. This approach has been applied to a set of peptides derived from typtic digestion of electrophoretically separated sea urchin egg membrane proteins. When directed to proteins that have been described previously, the results were in essential agreement with those obtained by conventional data base searching approaches, with certain important exceptions. The present method detected errors in published sequences and was able to develop sequences from peptides differing in mass by one dalton (Da). These results show both the power of the present approach and the need for using de novo methods more frequently than may be otherwise appreciated.
Yergey
Alfred L
AL
Laboratory of Cellular and Molecular Biophysics, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA. aly@helix.nih.gov
Coorssen
Jens R
JR
Backlund
Peter S
PS
Blank
Paul S
PS
Humphrey
Glen A
GA
Zimmerberg
Joshua
J
Campbell
Jennifer M
JM
Vestal
Marvin L
ML
D000465:Algorithms; D000803:Angiotensin I / Q000032:analysis; D000818:Animals; D004591:Electrophoresis, Polyacrylamide Gel; D008565:Membrane Proteins / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011492:Protein Hydrolysates / Q000737:chemistry; D012617:Sea Urchins; D017421:Sequence Analysis / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014357:Trypsin
D008565:Membrane Proteins; D010455:Peptides; D011492:Protein Hydrolysates; D000803:Angiotensin I; D014357:Trypsin