A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2004
| Date | 2004-12-01 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1016/j.jasms.2004.08.010 |
| Citations (OpenAlex) | 50 |
| Venue 2-year citedness | 2.84 |
Abstract
The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have increased its application in recent years. The most common method of “peptide mass fingerprint” analysis often does not provide robust identification. Additional sequence information, obtained by post-source decay or collision induced dissociation, provides additional constraints for database searches. However, de novo sequencing by mass spectrometry is not yet common practice, most likely because of the difficulties associated with the interpretation of high and low energy CID spectra. Success with this type of sequencing requires full sequence coverage and demands better quality spectra than those typically used for data base searching. In this report we show that full-length de novo sequencing is possible using MALDI TOF/TOF analysis. The interpretation of MS/MS data is facilitated by N-terminal sulfonation after protection of lysine side chains (Keough et al., Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7131-7136). Reliable de novo sequence analysis has been obtained using sub-picomol quantities of peptides and peptide sequences of up to 16 amino acid residues in length have been determined. The simple, predictable fragmentation pattern allows routine de novo interpretation, either manually or using software. Characterization of the complete primary structure of a peptide is often hindered because of differences in fragmentation efficiencies and in specific fragmentation patterns for different peptides. These differences are controlled by various structural parameters including the nature of the residues present. The influence of the presence of internal Pro, acidic and basic residues on the TOF/TOF fragmentation pattern will be discussed, both for underivatized and guanidinated/sulfonated peptides.
Methods and tools
- N-sulfonated peptide MALDI TOF/TOF de novo sequencing: N-sulfonation before MALDI TOF/TOF directs fragmentation into a single dominant series, so a peptide mass fingerprint that does not identify a protein on its own can be followed by a readable de novo spectrum.
Cites (6)
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- Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry (2000) crossref
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Cited by (4)
- De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature (2012) crossref
- <i>De novo</i> sequencing of two new cyclic <i>θ</i> ‐defensins from baboon ( <i>Papio hamadryas</i> ) leukocytes by matrix‐assisted laser desorption/ionization mass spectrometry (2010) crossref
- De novo sequencing of peptides by MS/MS (2010) crossref
- De novo protein sequence analysis of Macaca mulatta (2007) semanticscholar