Y. Ishihama

This paper introduces a centrifugal gel crushing method to improve protein recovery and reproducibility in gel-based proteomics by replacing manual dicing with a pipette tip-based technique.

This paper introduces a proteomic method to identify endogenous lipidation sites using liquid-liquid extraction and mass spectrometry, finding 90 sites in HeLa cells and tissue-specific profiles in mice.

The paper investigates phosphorylation motifs of three kinases using cell-extracted proteomes as substrate pools and finds consistent motifs across different cell lines.

This study demonstrates that F2Pmp probes can enrich PTPs based on their activity, revealing fluctuations in PTPN1 and PTPN2 activities and establishing a tool for activity-based tyrosine phosphatomics.

This study identifies proteases regulating beige adipocyte differentiation through N-terminomics and functional experiments.

pSNAP profiles proteome-wide elongating nascent polypeptide chains, revealing translational repression and modification effects on ribosome-associated interactions.

This paper introduces a novel lectin-based affinity chromatography method using spongy monoliths to classify extracellular vesicles based on surface glycan structures and demonstrates subpopulations through proteome profiling.

The paper develops a one-step method to isolate protein C-terminal peptides using MOLEX chromatography, achieving high purity and coverage in human C-terminomics.

This study identifies a novel interaction between Regnase-1 and 14-3-3 mediated by IRAK1 that stabilizes inflammatory mRNAs by inhibiting Regnase-1 activity.

This study introduces a proteomic method to quantify mitochondrial-encoded proteins and reveals post-translational regulation of OXPHOS complexes.

This study systematically characterizes how phosphorylation affects collision cross sections of peptides in ion mobility spectrometry, finding that phosphorylation can reduce CCS despite increasing mass.

The paper introduces a method to enrich and profile protein N-terminal peptides using TrypN digestion and CHAMP-SCX chromatography, achieving high specificity and sensitivity in human cell lysates.

This paper introduces a method to accurately quantify nascent proteins by dual pulse labeling with OPP and stable isotope labeled amino acids, revealing repression of specific proteins upon transcription inhibition.