PXD012738
PXD012738 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | LysargiNase Enhances the Protein Identification on FFPE Samples |
| Description | Formalin-Fixed Paraffin-Embedded (FFPE) samples are treasure for proteomic studies of disease. However, their usage is hampered for proteomics study because of the crosslink among proteins, and protein vs nucleic acid. Even worse, other covalent chemical modifications like methylation introduced by formaldehyde interfere trypsin digestion. We applied LysargiNase for the first time in FFPE samples, and systematically compared the samples digested by LysargiNase with commonly used tryptic samples. A total of 33095 peptides and 3559 proteins were identified with LysargiNase and trypsin combined in two replicates. LysargiNase increased peptide identification by 19.3% and protein identification by 13.3% on the basis of trypsin. Consistently, LysargiNase increased C terminal peptide identification by 47.7%. Moreover, LysargiNase showed less missed-cleavage rate (54.5%) at methylated sites than trypsin (74.5%), contributing to the identification of methylated peptides in FFPE samples. |
| HostingRepository | iProX |
| AnnounceDate | 2019-02-15 |
| AnnouncementXML | Submission_2019-05-15_20:50:48.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Shu Liu |
| SpeciesList | scientific name: Mus musculus; NCBI TaxID: 10090; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | LTQ Orbitrap Velos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2019-02-17 07:37:29 | ID requested | |
| ⏵ 1 | 2019-05-15 20:50:49 | announced |
Publication List
| Liu S, Xu F, Yin Y, Zhang J, Wang F, Li Y, Xu P, LysargiNase enhances protein identification on the basis of trypsin on formalin-fixed paraffin-embedded samples. Rapid Commun Mass Spectrom, 33(17):1381-1389(2019) [pubmed] |
Keyword List
| submitter keyword: FFPE, proteome, Trypsin, LysargiNase, methylation, mouse liver |
Contact List
| Ping Xu | |
|---|---|
| contact affiliation | National Center for Protein Sciences (Beijing) |
| contact email | xuping@mail.ncpsb.org |
| lab head | |
| Shu Liu | |
| contact affiliation | National Center for Protein Sciences (Beijing) |
| contact email | liushulr@126.com |
| dataset submitter | |
Full Dataset Link List
| iProX dataset URI |
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