Proteomics

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Rapid and Label-Free Structural Proteomics by One-Step Swift Trypsin LiP-MS


ABSTRACT: We developed a rapid, surface-targeted limited proteolysis workflow, Swift Trypsin LiP-MS (STLiP-MS), to profile proteome-wide structural changes under near-native conditions. STLiP-MS uses a trypsin-immobilized spin column and centrifugation-controlled contact to achieve instantaneous, highly reproducible limited digestion, followed by reduction/alkylation and desalting. Proof-of-concept analyses were performed on HEK293T cell lysates (± phosphatase inhibitor PhosSTOP) and on a purified GPCR complex (A2A-BRIL with IgG). Peptides were separated on a 75-µm ID C18 column (50 °C) using an UltiMate 3000 RSLCnano and analyzed on an Orbitrap HF-X. Both DDA (top-50 HCD, 70-min gradient) and DIA (variable windows, 70-min gradient) runs were acquired. DIA data were processed with DIA-NN (library-free/in-silico; UniProt human, 2024-03), and DDA of purified samples with PEAKS Studio 12.5.

ORGANISM(S): Homo Sapiens (human) Cellular Organisms

SUBMITTER: Yusuke Kawashima 

PROVIDER: PXD069771 | JPOST Repository | Mon Jan 05 00:00:00 GMT 2026

REPOSITORIES: jPOST

Dataset's files

Source:
Action DRS
240524_miya-7_Temp4-1.raw Raw
240524_miya-7_Temp4-2.raw Raw
240524_miya-7_Temp4-3.raw Raw
240524_miya-7_Temp4-4.raw Raw
240524_miya-8_Temp4_stop-1.raw Raw
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Publications

Rapid and Label-Free Structural Proteomics Using One-Step Swift Trypsin LiP-MS.

Miyashita Yasuomi Y   Konno Ryo R   Ogasawara Satoshi S   Okuda Yusei Y   Takamuku Yuuki Y   Moriya Toshio T   Saito Tetsuichiro T   Murata Takeshi T   Ohara Osamu O   Kawashima Yusuke Y  

ACS omega 20251225 1


Limited proteolysis mass spectrometry (LiP-MS) is a powerful approach for probing protein conformational changes on a proteome-wide scale. However, conventional workflows rely on a two-step digestion with proteinase K and trypsin, which increases complexity and reduces reproducibility and sensitivity. This study aimed to develop a simplified one-step protocol, termed Swift Trypsin LiP-MS (STLiP-MS), which uses a trypsin-immobilized spin column and high-speed centrifugation to achieve rapid and r  ...[more]

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