PXD004604
PXD004604 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Phosphoproteome Analysis of Formalin-Fixed and Paraffin-Embedded Tissue Sections Mounted on Microscope Slides |
| Description | Formalin-fixed and paraffin-embedded (FFPE) sections mounted on microscope slides are one of the largest available resources for retrospective research on various diseases, but quantitative phosphoproteome analysis of FFPE sections has never been achieved because of the extreme difficulty of procuring sufficient phosphopeptides from the limited amounts of proteins on the slides. Here, we present the first protocol for quantitative phosphoproteome analysis of FFPE sections by utilizing phase-transfer surfactant-aided extraction/tryptic digestion of FFPE proteins followed by high-recovery phosphopeptide enrichment via lactic acid-modified titania chromatography. We established that FFPE sections retain a similar phosphoproteome to fresh tissue specimens during storage for at least 9 months, confirming the utility of our method for evaluating phosphorylation profiles in various diseases. We also verified that chemical labeling based on reductive dimethylation of amino groups was feasible for quantitative phosphoproteome analysis of FFPE samples on slides. Furthermore, we improved the LC–MS sensitivity by miniaturizing nanoLC columns to 25 μm inner diameter. With this system, we could identify 1090 phosphopeptides from a single FFPE section obtained from a microscope slide, containing 25.2 ± 5.4 μg of proteins. This protocol should be useful for large-scale phosphoproteome analysis of archival FFPE slides, especially scarce samples from patients with rare diseases. |
| HostingRepository | jPOST |
| AnnounceDate | 2016-07-20 |
| AnnouncementXML | Submission_2022-11-22_00:53:27.686.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Hironori Achiwa |
| SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
| ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine |
| Instrument | TripleTOF 5600 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2016-07-19 20:02:21 | ID requested | |
| 1 | 2016-07-19 20:07:15 | announced | |
| 2 | 2016-07-20 00:41:17 | announced | Updated Announce date and Modification list. |
| 3 | 2018-09-18 22:36:42 | announced | Updated CV, FTP location and Modification list. |
| 4 | 2021-02-04 16:47:20 | announced | 2021-02-04: Updated FTP location. |
| 5 | 2022-09-18 02:23:48 | announced | 2022-09-18: Updated FTP location. |
| ⏵ 6 | 2022-11-22 00:53:28 | announced | 2022-11-22: Updated PubMed. |
Publication List
| Wakabayashi M, Yoshihara H, Masuda T, Tsukahara M, Sugiyama N, Ishihama Y, Phosphoproteome analysis of formalin-fixed and paraffin-embedded tissue sections mounted on microscope slides. J Proteome Res, 13(2):915-24(2014) [pubmed] |
Keyword List
| submitter keyword: FFPE slide |
| formalin-fixed and paraffin-embedded |
| phase-transfer surfactant |
| phosphoproteome analysis |
| post-translational modifications |
| protein extraction |
| shotgun analysis |
Contact List
| Yasushi Ishihama | |
|---|---|
| lab head | |
| Hironori Achiwa | |
| contact affiliation | Kyoto Univ. |
| 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/JPST000084/ |
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