“De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2003
| Date | 2003-12-01 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1016/S1044-0305(03)00346-5 |
| Citations (OpenAlex) | 22 |
| Venue 2-year citedness | 2.84 |
Abstract
Collision-induced dissociation of singly charged peptide ions produced by resonant excitation in a matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer yields relatively low complexity MS/MS spectra that exhibit highly preferential fragmentation, typically occurring adjacent to aspartyl, glutamyl, and prolyl residues. Although these spectra have proven to be of considerable utility for database-driven protein identification, they have generally been considered to contain insufficient information to be useful for extensive de novo sequencing. Here, we report a procedure for de novo sequencing of peptides that uses MS/MS data generated by an in-house assembled MALDI-quadrupole-ion trap mass spectrometer (Krutchinsky, Kalkum, and Chait Anal. Chem. 2001, 73, 5066-5077). Peptide sequences of up 14 amino acid residues in length have been deduced from digests of proteins separated by SDS-PAGE. Key to the success of the current procedure is an ability to obtain MS/MS spectra with high signal-to-noise ratios and to efficiently detect relatively low abundance fragment ions that result from the less favorable fragmentation pathways. The high signal-to-noise ratio yields sufficiently accurate mass differences to allow unambiguous amino acid sequence assignments (with a few exceptions), and the efficient detection of low abundance fragment ions allows continuous reads through moderately long stretches of sequence. Finally, we show how the aforementioned preferential cleavage property of singly charged ions can be used to facilitate the de novo sequencing process.
Methods and tools
- MALDI-QIT de novo sequencing: Preliminary MALDI-QIT de novo
Cites (15)
- De novo sequencing of peptides using MALDI/TOF-TOF (2002) crossref
- De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging (2002) crossref
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) crossref
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) crossref
- Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching (2001) crossref
- Automatedde novo sequencing of proteins using the differential scanning technique (2001) crossref
- Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry (2000) crossref
- Quantitation and Facilitated de Novo Sequencing of Proteins by Isotopic N-Terminal Labeling of Peptides with a Fragmentation-Directing Moiety (2000) crossref
- De Novo Peptide Sequencing by Two-Dimensional Fragment Correlation Mass Spectrometry (2000) crossref
- Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (2000) crossref
- Evaluation of charge derivatization of a proteolytic protein digest for improved mass spectrometric analysis:de novo sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry (1999) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
- A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry (1999) crossref
- De novo peptide sequencing in an ion trap mass spectrometer with 18O labeling (1998) crossref
- Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997) crossref
Cited by (6)
- De novo sequence analysis and intact mass measurements for characterization of phycocyanin subunit isoforms from the blue‐green alga Aphanizomenon flos‐aquae (2009) crossref
- How much peptide sequence information is contained in ion trap tandem mass spectra? (2008) crossref
- De novo sequencing of a 21‐kDa cytochrome c4 from Thiocapsa roseopersicina by nanoelectrospray ionization ion‐trap and Fourier‐transform ion‐cyclotron resonance mass spectrometry (2007) crossref
- De novo protein sequence analysis of Macaca mulatta (2007) semanticscholar
- A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry (2004) crossref
- Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry (2004) crossref