De Novo Sequencing of Unique Sequence Tags for Discovery of Post-Translational Modifications of Proteins
peer-reviewed · Analytical Chemistry · 2008
| Date | 2008-10-15 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1021/ac801123p |
| Citations (OpenAlex) | 36 |
| Venue 2-year citedness | 7.10 |
Abstract
De novo sequencing is a spectrum analysis approach for mass spectrometry data to discover post-translational modifications in proteins; however, such an approach is still in its infancy and is still not widely applied to proteomic practices due to its limited reliability. In this work, we describe a de novo sequencing approach for the discovery of protein modifications based on identification of the proteome UStags (Shen, Y.; Tolić, N.; Hixson, K. K.; Purvine, S. O.; Pasa-Tolić, L.; Qian, W. J.; Adkins, J. N.; Moore, R. J.; Smith, R. D. Anal. Chem. 2008, 80, 1871-1882). The de novo information was obtained from Fourier-transform tandem mass spectrometry data for peptides and polypeptides from a yeast lysate, and the de novo sequences obtained were selected based on filter levels designed to provide a limited yet high quality subset of UStags. The DNA-predicted database protein sequences were then compared to the UStags, and the differences observed across or in the UStags (i.e., the UStags’ prefix and suffix sequences and the UStags themselves) were used to infer possible sequence modifications. With this de novo-UStag approach, we uncovered some unexpected variances within several yeast protein sequences due to amino acid mutations and/or multiple modifications to the predicted protein sequences. To determine false discovery rates, two random (false) databases were independently used for sequence matching, and ~3% false discovery rates were estimated for the de novo-UStag approach. The factors affecting the reliability (e.g., existence of de novo sequencing noise residues and redundant sequences) and the sensitivity of the approach were investigated and described. The combined de novo-UStag approach complements the UStag method previously reported by enabling the discovery of new protein modifications.
Methods and tools
- Unique sequence tags for PTM discovery: Reads short, uniquely assignable sequence tags de novo and uses them to find post-translational modifications, trading the full-length sequence for the reliability that made early de novo output hard to trust in routine proteomics.
Cites (5)
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) crossref
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) crossref
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) crossref
- Proteomics-Grade de Novo Sequencing Approach (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
Cited by (9)
- Validation of De Novo Peptide Sequences with Bottom-Up Tag Convolution (2021) both
- De novo sequencing of proteins by mass spectrometry (2020) both
- De Novo Sequencing of Proteins and Peptides: Algorithms, Applications, Perspectives (2018) crossref
- Antibody de novo Sequencing (2017) crossref
- De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra (2015) crossref
- Shotgun Protein Sequencing with Meta-contig Assembly (2012) both
- ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity (2011) both
- Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de novo-Protein Unique Sequence Tags Approach (2010) both
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both