Yasushi Ishihama

This paper introduces two modified CHAMP-N methods to extend N-terminal peptide length, improving N-terminome coverage while maintaining technical reproducibility.

The paper identifies phosphorylation sites that regulate protein interactions using pan-cancer data and AlphaFold predictions, revealing 6,160 associations between phosphosites and interacting protein abundance.

The paper introduces DiReCT, a method to improve peptide solubility and recovery for nanoHILIC/MS/MS proteomics by integrating solubilization and elution in a single StageTip workflow.

This paper introduces a method to detect protein conformational changes on a proteome-wide scale using kinase-mediated phosphorylation and phosphoproteomics.

This paper introduces Rapid HAMMOC, a phosphoproteomics workflow that improves sensitivity and reduces sample loss, identifying more phosphosites from low-input samples.

This paper evaluates two SDB-containing PTFE disks for proteomics, finding one provides better peptide recovery, especially for low-input samples.

This study demonstrates that protease type XIII from Aspergillus saitoi improves bottom-up proteomics under acidic conditions by enhancing sequence coverage and reducing modification artifacts compared to trypsin.

UniScore integrates and standardizes outputs from multiple search engines in proteomics, outperforming single search engines in large-scale data analysis.

The paper introduces a pretrained deep protein language model for predicting peptide collision cross sections, reducing training time while maintaining or improving prediction performance.

This paper introduces a desalting tip column (ChocoTip) that improves peptide recovery in proteomics, outperforming existing methods in sensitivity and coverage.

This study develops a timing-controllable m6A demethylation tool with reduced off-target effects by combining PUF RNA-binding proteins with m6A-erasers and a rapamycin-based switch.

The paper develops a protein half-life prediction model, PLTNUM, using a protein language model trained on NIH3T3 mouse data, achieving 71% accuracy and identifying key sequence features affecting half-life.

The paper introduces a one-step N-terminomics method using tip-based SCX chromatography, enabling high-throughput and sensitive profiling of N-terminal peptides.

The paper investigates how pathogenic mutations at phosphorylation sites affect protein-protein interactions, showing that such mutations disrupt phosphorylation-dependent motifs and alter cellular functions.

This paper describes a method to coat living cell membranes onto nanoparticles, demonstrating improved biocompatibility and reduced phagocytosis.

The paper investigates ribosome ubiquitination dynamics during zebrafish development, identifying Znf598-mediated ubiquitination of Rps10/eS10 as a key regulatory mechanism.

The paper introduces hybrid-DIA, a method combining targeted and discovery phosphoproteomics for single spheroids, showing comparable accuracy to existing methods while profiling the global phosphoproteome.

This paper develops a high-speed LC/MS/MS system achieving 1,000 samples per day with high sensitivity and depth, demonstrating its application in spatial proteomics of mouse brain.

The paper generates a comprehensive atlas of alternative splicing in human immune cells using long-read sequencing, identifies unannotated transcripts, and links isoforms to disease through quantitative trait loci and GWAS data.

The paper introduces a motif-centric phosphoproteomics approach to quantify phosphorylation pathways using in vitro kinase reactions and isobaric labeling, demonstrating selective quantification of over 7,000 tyrosine phosphorylation sites.

This study investigates the role of small extracellular vesicles in regulating neural stem cell quiescence and proliferation, finding that exosome inhibition affects cell cycle entry and maintenance of quiescence.

The paper develops a sequence-specific model to predict peptide collision cross-section values using amino-acid sequence and charge state information from proteomic data.

This paper introduces a statistical method for joint peptide and protein identification and quantification in proteomics using mass spectrogram decomposition, showing improved accuracy compared to conventional approaches.

The paper identifies cleavage sites of ectodomain shedding in 10 human cell lines using mass spectrometry and finds 411 cleavage sites on 132 membrane proteins.

This study identifies RseP as an intramembrane protease that cleaves FecR, a regulator of ferric citrate uptake, revealing a novel role in iron homeostasis in E. coli.

This study identifies endogenous kinase substrates using proximity labeling and phosphoproteomics, finding 33 CK2 and 52 PKA substrates and linking mutations to altered phosphorylation.