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PXD064095
PXD064095 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | All under acidic bottom-up proteomics using protease type XIII from Aspergillus Saitoi |
| Description | Bottom-up proteomics is a powerful technique for comprehensive analysis of proteins by cleaving them into peptides with proteases and analysing them by liquid chromatography/tandem mass spectrometry. Trypsin is the gold standard protease for bottom-up proteomics, however its cleavage specificity limits peptide identification depending on the protein sequence. In addition, its optimal pH conditions are weakly alkaline, which can cause modification artifacts such as deamidation. In addressing these limitations, we have investigated the potential of protease type XIII (P13ase) from Aspergillus saitoi, which is active at low pH. P13ase has been used for protein structural analysis by hydrogen deuterium exchange mass spectrometry, but its cleavage preferences has not been clarified. In this study, we found that the optimal P13ase digestion conditions for bottom-up proteomics are pH 3.5, 37°C for 60 min, and that P13ase primarily cleaves the C-terminal side of Lys, Arg, and Leu. When this optimal digestion condition was applied to HeLa cell extracts and compared to trypsin, it was possible to achieve sequence coverage of more than 90% for several proteins, which is unachievable with trypsin. In addition, P13ase digestion reduced artifacts such as deamidation products caused by cyclization reactions and subsequent hydrolysis. The results of this study support the high potential of P13ase as a new tool for precision proteomics. |
| HostingRepository | jPOST |
| AnnounceDate | 2025-11-28 |
| AnnouncementXML | Submission_2025-11-28_05:05:55.236.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Ryota Tomioka |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide; deamidated L-asparagine; Ammonia-loss |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-05-20 02:55:42 | ID requested | |
| ⏵ 1 | 2025-11-28 05:05:56 | announced |
Publication List
| Tomioka R, Tomioka A, Ogata K, Ishihama Y, Bottom-Up Proteomics Under Acidic Conditions Using Protease Type XIII From Aspergillus saitoi. Mol Cell Proteomics, 25(1):101469(2025) [pubmed] |
Keyword List
| submitter keyword: Protease type XIII, Bottom-up proteomics, Protease, Deamidation, Cleavage preference |
Contact List
| Yasushi Ishihama | |
|---|---|
| lab head | |
| Ryota Tomioka | |
| contact affiliation | Kyoto university |
| dataset submitter | |
Full Dataset Link List
| jPOST dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST003814/ |
