PEPPI-MS: gel-based sample pre-fractionation for deep top-down and middle-down proteomics

A Takemori, PT Kaulich, A Tholey, N Takemori - Nature Protocols, 2025 - nature.com
Top-down analysis of intact proteins and middle-down analysis of proteins subjected to
limited digestion require efficient detection of traces of proteoforms in samples, necessitating …

Diversifying the concept of model organisms in the age of-omics

F Bertile, S Matallana-Surget, A Tholey… - Communications …, 2023 - nature.com
In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a
few historically well-established organisms, eg laboratory rodents, have enabled significant …

Modulation of α-synuclein in vitro aggregation kinetics by its alternative splice isoforms

A Röntgen, Z Toprakcioglu… - Proceedings of the …, 2024 - National Acad Sciences
The misfolding and aggregation of α-synuclein is linked to a family of neurodegenerative
disorders known as synucleinopathies, the most prominent of which is Parkinson's disease …

Mass spectrometry-based proteomic technology and its application to study skeletal muscle cell biology

P Dowling, D Swandulla, K Ohlendieck - Cells, 2023 - mdpi.com
Voluntary striated muscles are characterized by a highly complex and dynamic proteome
that efficiently adapts to changed physiological demands or alters considerably during …

IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection

JA Korchak, ED Jeffery, S Bandyopadhyay… - Journal of the …, 2024 - ACS Publications
Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which
transcript isoforms are translated into stable, functional protein isoforms is unclear …

Soil microbiome characterization and its future directions with biosensing

L DeFord, JY Yoon - Journal of Biological Engineering, 2024 - Springer
Soil microbiome characterization is typically achieved with next-generation sequencing
(NGS) techniques. Metabarcoding is very common, and meta-omics is growing in popularity …

Principal Component Analysis of Alternative Splicing Profiles Revealed by Long-Read ONT Sequencing in Human Liver Tissue and Hepatocyte-Derived HepG2 and …

E Sarygina, A Kozlova, K Deinichenko… - International Journal of …, 2023 - mdpi.com
The long-read RNA sequencing developed by Oxford Nanopore Technology provides a
direct quantification of transcript isoforms. That makes the number of transcript isoforms per …

Gel-Based Sample Fractionation with SP3-Purification for Top-Down Proteomics

A Takemori, N Sugiyama, JT Kline… - Journal of Proteome …, 2024 - ACS Publications
Precise prefractionation of proteome samples is a potent method for realizing in-depth
analysis in top-down proteomics. PEPPI-MS (Passively Eluting Proteins from Polyacrylamide …

[HTML][HTML] Addressing Diagnostic Gaps and Priorities of the Global Rare Diseases Community: Recommendations from the IRDiRC Diagnostics Scientific Committee

DR Adams, CDM van Karnebeek, SB Agullo… - European Journal of …, 2024 - Elsevier
ABSTRACT The International Rare Diseases Research Consortium (IRDiRC) Diagnostic
Scientific Committee (DSC) is charged with discussion and contribution to progress on …

Full-length transcriptome characterization and analysis of Carrizo Citrange and molecular insights into pathogen defense

R Li, Y Hu, X Wang, C Liu, G Huang - Molecular Genetics and Genomics, 2024 - Springer
Citrus huanglongbing (HLB) is a major challenge that impacts the flourishing of the citrus
industry. Therefore, analyzing the genomic information of HLB-resistant or tolerant citrus …