Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry
peer-reviewed · Proceedings of the National Academy of Sciences · 2000
| Date | 2000-09-12 |
| Type | peer-reviewed |
| Venue | Proceedings of the National Academy of Sciences |
| Publisher | National Academy of Sciences |
| Contribution | algorithm |
| DOI | 10.1073/pnas.97.19.10313 |
| Citations (OpenAlex) | 243 |
| Venue 2-year citedness | 8.56 |
Abstract
A de novo sequencing program for proteins is described that uses tandem MS data from electron capture dissociation and collisionally activated dissociation of electrosprayed protein ions. Computer automation is used to convert the fragment ion mass values derived from these spectra into the most probable protein sequence, without distinguishing Leu/Ile. Minimum human input is necessary for the data reduction and interpretation. No extra chemistry is necessary to distinguish N- and C-terminal fragments in the mass spectra, as this is determined from the electron capture dissociation data. With parts-per-million mass accuracy (now available by using higher field Fourier transform MS instruments), the complete sequences of ubiquitin (8.6 kDa) and melittin (2.8 kDa) were predicted correctly by the program. The data available also provided 91% of the cytochrome c (12.4 kDa) sequence (essentially complete except for the tandem MS-resistant region K(13)-V(20) that contains the cyclic heme). Uncorrected mass values from a 6-T instrument still gave 86% of the sequence for ubiquitin, except for distinguishing Gln/Lys. Extensive sequencing of larger proteins should be possible by applying the algorithm to pieces of approximately 10-kDa size, such as products of limited proteolysis.
Methods and tools
- ECD/CAD automated protein de novo sequencing: Program that converts high-resolution ECD and CAD fragment masses of intact protein ions into the most probable protein sequence, using ECD to tell N- from C-terminal fragments.
Cites (3)
- A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry (1999) crossref
- Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref
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