Research summary
The SEQUEST algorithm correlates uninterpreted tandem mass spectra of peptides produced under 10-50 eV collision conditions with amino-acid sequences from the Genpept database by searching within +/-1 u of precursor mass and computing a cross-correlation between predicted and observed fragment-ion m/z values, with a normalized cross-correlation difference >0.1 indicating a high-confidence match [1]. A statistical model of random sampling in shotgun proteomics described data-dependent acquisition as an incomplete sampling process in whole-cell-lysate analyses and showed how the model can be used both to predict expected sampling levels for mixtures of given complexity and to estimate relative protein abundance [2]. Multidimensional Protein Identification Technology (MudPIT) combined strong-cation-exchange and reversed-phase chromatography in a biphasic column with electrospray ionization tandem mass spectrometry, automating shotgun proteomics on thousands of peptides per analysis [3]. A review of shotgun/bottom-up proteomics surveyed sample preparation, separation, mass-spectrometric acquisition, database search and quantification approaches for protein analysis [4]. DTASelect assembles SEQUEST identifications into protein lists and highlights the most significant matches, while the companion Contrast tool enables cross-experiment comparison of DTASelect outputs to accelerate proteomic data analysis [5].
Recent publications
- An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseDOI
- Large-scale analysis of the yeast proteome by multidimensional protein identification technologyDOI
- Microglia Promote Learning-Dependent Synapse Formation through Brain-Derived Neurotrophic FactorDOI
- A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun ProteomicsDOI
- Wnt proteins are lipid-modified and can act as stem cell growth factorsDOI
- Direct analysis of protein complexes using mass spectrometryDOI
- An Automated Multidimensional Protein Identification Technology for Shotgun ProteomicsDOI
- Protein Analysis by Shotgun/Bottom-up ProteomicsDOI
- DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun ProteomicsDOI
- Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic TranscriptionDOI
The lab page does not clearly state student acceptance status. Email the professor directly to confirm.
How to apply
Email John R. Yates 6-12 months before your application deadline. Read several recent papers and reference specific work in your message. Use our how to email a Japanese professor guide for the proven email structure.
For applications via MEXT scholarship: see our MEXT 2027 complete guide and university-specific University Recommendation track.
External profiles
- ORCID: https://orcid.org/0000-0001-5267-1672
- OpenAlex: openalex.org
Profile compiled from public sources (Researchmap, OpenAlex, Osaka University faculty directory). Last refreshed 2026-05. Report incorrect information.