Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry
peer-reviewed · Analytical Chemistry · 2001
| Date | 2001-06-01 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | ACS |
| Contribution | algorithm |
| DOI | 10.1021/ac001196o |
| Citations (OpenAlex) | 293 |
| Venue 2-year citedness | 6.29 |
Abstract
There are several computer programs that can match peptide tandem mass spectrometry data to their exactly corresponding database sequences, and in most protein identification projects, these programs are utilized in the early stages of data interpretation. However, situations frequently arise where tandem mass spectral data cannot be correlated with any database sequences. In these cases, the unmatched data could be due to peptides derived from novel proteins, allelic or species-derived variants of known proteins, or posttranslational or chemical modifications. Two additional problems are frequently encountered in high-throughput protein identification. First, it is difficult to quickly sift through large amounts of data to identify those spectra that, due to poor signal or contaminants, can be ignored. Second, it is important to find incorrect database matches (false positives). We have chosen to address these difficulties by performing automatic de novo sequencing using a computer program called Lutefisk. Sequence candidates obtained are used as input in a homology-based database search program called CIDentify to identify variants of known proteins. Comparison of database-derived sequences with de novo sequences allows for electronic validation of database matches even if the latter are not completely correct. Modifications to the original Lutefisk program have been implemented to handle data obtained from triple quadrupole, ion trap, and quadrupole/time-of-flight hybrid (Qtof) mass spectrometers. For example, the linearity of mass errors due to temperature-dependent expansion of the flight tube in a Qtof was exploited such that isobaric amino acids (glutamine/lysine and oxidized methionine/ phenylalanine) can be differentiated without careful attention to mass calibration.
Methods and tools
- Lutefisk: First widely-used heuristic de novo tool
Cites (4)
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Cited by (32)
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- Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) both
- SeqNovo: De Novo Peptide Sequencing Prediction in IoMT via Seq2Seq (2023) crossref
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- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013) both
- Constrained De Novo Sequencing of Conotoxins (2012) both
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- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) crossref
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) semanticscholar
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both
- De novo sequencing of peptides by MS/MS (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
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- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides (2007) crossref
- Assessing peptide de novo sequencing algorithms performance on large and diverse data sets (2007) crossref
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- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- De novo sequencing of peptides using MALDI/TOF-TOF (2002) both