Y. Ishihama

One-step N-terminomics based on isolation of protein N-terminal peptides from LysargiNase digests by tip-based strong cation exchange chromatography

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

Centrifugal Gel Crushing for Gel-based Proteome Analysis

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.

Liquid-liquid extraction of lipidated peptides for direct identification of lipidation sites

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.

Validity of the cell-extracted proteome as a substrate pool for exploring phosphorylation motifs of kinases

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

Activity-based tyrosine phosphatomics using F2Pmp probes

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.

Protein N-Terminomics Reveals Major Proteases in Regulating Beige Adipocyte Differentiation

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

Classification of Extracellular Vesicles based on Surface Glycan Structures by Spongy-like Separation Media

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.

pSNAP: Proteome-wide analysis of elongating nascent polypeptide chains

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

One-step Isolation of Protein C-terminal Peptides from V8 Protease-digested Proteins by Metal Oxide-based Ligand Exchange Chromatography

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.

IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay

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.

Monitoring mitochondrial translation by pulse SILAC

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

Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry

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.

Isolation of protein N-terminal peptides by charge-mediated position- elective enrichment using strong cation exchange chromatography

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.

Quantitative nascent proteome profiling by dual pulse labeling with O-propargyl-puromycin and stable isotope labeled amino acids

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.