PXD000049-2
PXD000049 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Comparative phosphoproteome of Trypanosoma brucei bloodstream & procyclic form |
| Description | Comparative phosphoproteomic analysis of SILAC labelled cultured bloodstream and procyclic form Trypansoma brucei. Phosphopeptide enrichement via SCX and TiO2, acquired on Oribtrap Velos using MSA. Triplicate biological replicate for each lifecycle stage (as unmixed, and two SILAC label swap expreiments), eight fraction injected in technical triplicate. For the SILAC labelled samples, the corresponding changes in the proteome were measured using unenriched peptides sperated by SCX. Data was processed using MaxQuant version 1.3.0.5 which incorporates the Andromeda search engine. Proteins were identified by searching a protein sequence database containingT. brucei brucei 927 annotated proteins (Version 4.0, downloaded from TriTrypDB http://www.tritrypdb.org/ supplemented with the VSG221 sequence and frequently observed contaminants (porcine trypsin, bovine serum albumins and mammalian keratins) that contains a total of 10,081 protein sequences. Search parameters specified an MS tolerance of 6 ppm, an MS/MS tolerance at 0.5 Da and full trypsin specificity, allowing for up to two missed cleavages. Carbamidomethylation of cysteine was set as a fixed modification and oxidation of methionines, N-terminal protein acetylation and N-pyroglutamate were allowed as variable modifications. Phosphoproteomic analysis included phosophorylation of serine, threonine and tyrosine as additional variable modifications. Peptides were required to be at least 7 amino acids in length and a MaxQuant score >5, with false discovery rates (FDRs) of 0.01 calculated at the levels of peptides, proteins and modification sites based on the number of hits against the reversed sequence database. |
| HostingRepository | PRIDE |
| AnnounceDate | 2013-07-03 |
| AnnouncementXML | Submission_2013-07-03_07:24:03.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Michael Urbaniak |
| SpeciesList | scientific name: Trypanosoma brucei; NCBI TaxID: 5691; |
| ModificationList | phosphorylated residue; iodoacetamide derivatized residue; monohydroxylated residue; acetylated residue; 2-pyrrolidone-5-carboxylic acid (Glu) |
| Instrument | LTQ Orbitrap Velos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2012-10-11 07:11:56 | ID requested | |
| 1 | 2013-07-03 07:19:28 | announced | |
| 1 | 2014-07-25 00:41:12 | announced | |
| ⏵ 2 | 2013-07-03 07:24:03 | announced | Add reference |
| 3 | 2024-10-22 03:58:52 | announced | 2024-10-22: Updated project metadata. |
Publication List
| Urbaniak MD, Martin DM, Ferguson MA, Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei. J Proteome Res, 12(5):2233-44(2013) [pubmed] |
Keyword List
| submitter keyword: Phosphoproteome, Trypanosoma brucei, SILAC |
Contact List
| Michael Urbaniak | |
|---|---|
| contact affiliation | School of Life Sciences |
| contact email | m.d.urbaniak@dundee.ac.uk |
Full Dataset Link List
| 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.pride.ebi.ac.uk/2013/07/PXD000049 |
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