Automatedde novo sequencing of proteins using the differential scanning technique
peer-reviewed · PROTEOMICS · 2001
| Date | 2001-04-01 |
| Type | peer-reviewed |
| Venue | PROTEOMICS |
| Publisher | Wiley |
| Contribution | algorithm |
| DOI | 10.1002/1615-9861(200104)1:5<668::aid-prot668>3.0.co;2-s |
| Citations (OpenAlex) | 45 |
Abstract
Despite the progress in genomic DNA sequencing de novo sequencing of peptides is still required in a biological research environment since many experiments are done in organisms whose genomes are not sequenced. A way to unambiguously retrieve a peptide sequence from a tandem mass spectrum is to assign the correct ion type to the fragments. Here we describe a method which improves the specificity in y-ion assignment throughout the spectrum. The differential scanning technique requires that the peptides are partially 18O labelled at their C-terminus and that two fragment spectra are acquired for each peptide, one selecting the 16O/18O isotopic cluster and a second fragmenting only the 18O labelled ions. When the spectra are acquired with a quadrupole time of flight mass spectrometer y-ions can be very specifically filtered from the spectrum using a computer algorithm. Partial or complete peptide sequences can be assigned automatically simply by finding the most abundant series of fragments spaced by amino acid residue masses. This method was used extensively in a project investigating vesicular transport in bovine brain cells. Human or mouse homologues to the bovine proteins were found in EST databases facilitating rapid cloning of the human homologues.
Methods and tools
- Differential scanning de novo sequencing: Resolves the ion-type ambiguity that makes a tandem mass spectrum hard to read by acquiring the same peptide under differing conditions and comparing the scans, so a fragment’s series can be assigned rather than inferred. Aimed at organisms whose genomes are not sequenced, where a database is not an option.
Cited by (17)
- Bromine isotopic signature facilitates de novo sequencing of peptides in free‐radical‐initiated peptide sequencing (FRIPS) mass spectrometry (2015) crossref
- A Simplified Method for Peptide De Novo Sequencing Using 18 O Labeling (2014) crossref
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Dimethyl isotope labeling assisted de novo peptide sequencing (2010) crossref
- EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2010) crossref
- De novo sequencing of peptides by MS/MS (2010) crossref
- Peptide de Novo Sequencing Facilitated by a Dual-Labeling Strategy (2005) crossref
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref
- Two-Dimensional Mass Spectra Generated from the Analysis of 15N-Labeled and Unlabeled Peptides for Efficient Protein Identification and de novo Peptide Sequencing (2004) crossref
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) crossref
- Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry (2004) crossref
- High-Throughput Identification of Proteins and Unanticipated Sequence Modifications Using a Mass-Based Alignment Algorithm for MS/MS de Novo Sequencing Results (2004) crossref
- The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches (2004) both
- “De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study (2003) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- Secondary Losses via γ-Lactam Formation in Hot Electron Capture Dissociation: A Missing Link to Complete de Novo Sequencing of Proteins? (2003) crossref