<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ProteomeXchangeDataset id="PXD047268" formatVersion="1.4.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.4.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<CvList>
<Cv fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" id="MS"/>
<Cv fullName="PSI-MOD" uri="https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo" id="MOD"/>
<Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
</CvList>
<ChangeLog>
<ChangeLogEntry date="2024-10-22">Updated project metadata.</ChangeLogEntry>
</ChangeLog>
<DatasetSummary announceDate="2024-10-22" hostingRepository="PRIDE" title="Probing the trypanosome nuclear pore by TurboID proximity labelling">
<Description>Previous BioID experiments targeting the nucleoporin (NUP) NUP158 and the nuclear transport factor MEX67 indicated (PMID: 36410438; PXD031245) that proximity labelling delivers highly specific interactome data in the confined localisation of the nuclear pore, with a labelling radius well below the size of the nuclear pore. Here we extended this approach to target NUPs NUP110, NUP76 and NUP96 with a TurboID-HA tandem tag fused to both, the N and C-terminus of each respective target protein. While the central NUP96 biotinylated most nuclear pore proteins with the marked exception of the nuclear basket, NUP158, NUP110 and NUP76 caused biotinylation of specific sub-complexes of the pore and Mex67 labelled NUPs lining the pore channel.</Description>
<ReviewLevel>
<cvParam cvRef="MS" accession="MS:1002854" name="Peer-reviewed dataset"/>
</ReviewLevel>
<RepositorySupport>
<cvParam cvRef="MS" accession="MS:1002857" name="Unsupported dataset by repository"/>
</RepositorySupport>
</DatasetSummary>
<DatasetIdentifierList>
<DatasetIdentifier>
<cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD047268"/>
<cvParam cvRef="MS" accession="MS:1001921" name="ProteomeXchange accession number version number" value="2"/>
</DatasetIdentifier>
</DatasetIdentifierList>
<DatasetOriginList>
<DatasetOrigin>
<cvParam cvRef="MS" accession="MS:1002868" name="Original data"/>
</DatasetOrigin>
</DatasetOriginList>
<SpeciesList>
<Species>
<cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Trypanosoma brucei"/>
<cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="5691"/>
</Species>
</SpeciesList>
<InstrumentList>
<Instrument id="Instrument_1">
<cvParam cvRef="MS" accession="MS:1002416" name="Orbitrap Fusion"/>
</Instrument>
</InstrumentList>
<ModificationList>
<cvParam cvRef="MOD" accession="MOD:00397" name="iodoacetamide derivatized residue"/>
</ModificationList>
<ContactList>
<Contact id="project_submitter">
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Martin Zoltner"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="m.zoltner@dundee.ac.uk"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Division of Biological Chemistry & Drug Discovery School of Life Sciences University of Dundee Dundee DD1 5EH"/>
<cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
</Contact>
<Contact id="project_lab_head">
<cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Dr. Martin Zoltner"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="zoltnerm@natur.cuni.cz"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Head of Drug Discovery and Evaluation Charles University in Prague, BIOCEV Průmyslová 595 252 50 Vestec Czech Republic phone: +420 325 873 966"/>
</Contact>
</ContactList>
<PublicationList>
<Publication id="PMID36410438">
<cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="36410438"/>
<cvParam cvRef="MS" accession="MS:1002866" name="Reference" value="Moreira CMDN, Kelemen CD, Obado SO, Zahedifard F, Zhang N, Holetz FB, Gauglitz L, Dallagiovanna B, Field MC, Kramer S, Zoltner M. Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared. J Biol Chem. 2023 299(1):102726"/>
</Publication>
<Publication id="DOI-10_1016_j_jbc_2022_102726">
<cvParam cvRef="MS" accession="MS:1001922" name="Digital Object Identifier (DOI)" value="10.1016/j.jbc.2022.102726"/>
</Publication>
</PublicationList>
<KeywordList>
<cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="BioID, Trypanosoma brucei, porin, nuclear transport, nuclear pore"/>
</KeywordList>
<FullDatasetLinkList>
<FullDatasetLink>
<cvParam cvRef="MS" accession="MS:1002852" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268"/>
</FullDatasetLink>
<FullDatasetLink>
<cvParam cvRef="MS" accession="MS:1001930" name="PRIDE project URI" value="http://www.ebi.ac.uk/pride/archive/projects/PXD047268"/>
</FullDatasetLink>
</FullDatasetLinkList>
<DatasetFileList>
<DatasetFile id="FILE_1" name="NUP110C_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP110C_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_2" name="NUP76N_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP76N_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_3" name="TriTrypDB-64_TbruceiTREU927_AnnotatedProteins.fasta">
<cvParam cvRef="MS" accession="MS:1002845" name="Associated file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/TriTrypDB-64_TbruceiTREU927_AnnotatedProteins.fasta"/>
</DatasetFile>
<DatasetFile id="FILE_4" name="NUP110N_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP110N_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_5" name="NUP96N_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP96N_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_6" name="checksum.txt">
<cvParam cvRef="MS" accession="MS:1002851" name="Other type file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/checksum.txt"/>
</DatasetFile>
<DatasetFile id="FILE_7" name="NUP76N_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP76N_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_8" name="NUP96N_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP96N_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_9" name="NUP76C_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP76C_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_10" name="NUP96C_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP96C_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_11" name="NUP110C_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP110C_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_12" name="NUP96C_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP96C_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_13" name="BioID_PCF_NUP110NUP76NUP96_output.txt.rar">
<cvParam cvRef="MS" accession="MS:1002849" name="Search engine output file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/BioID_PCF_NUP110NUP76NUP96_output.txt.rar"/>
</DatasetFile>
<DatasetFile id="FILE_14" name="NUP110N_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP110N_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_15" name="NUP76C_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD047268/NUP76C_2.raw"/>
</DatasetFile>
</DatasetFileList>
<RepositoryRecordList>
<RepositoryRecord name="Probing the trypanosome nuclear pore by TurboID proximity labelling" label="PRIDE project" recordID="PXD047268" repositoryID="PRIDE" uri="http://www.ebi.ac.uk/pride/archive/projects/PXD047268"/>
</RepositoryRecordList>
</ProteomeXchangeDataset>