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PXD020474

PXD020474 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSystems biology of blood and tissue for comprehensive analysis of immune response to hepatitis B vaccine in adults
DescriptionProtein concentrations of both lysed WBC and plasma samples were measured by the PierceTM Bradford Assay and normalized to contain 10 μg per sample before proceeding with sample digestion using the procedure as previously described44. Peptides were desalted using STop-And-Go Extraction tips (STAGE tips)45, dried using the Vacufuge Plus (Eppendorf) for 45 minutes, then chemically dimethylated with light, medium, and heavy formaldehyde46 for triplex analysis of each timepoint per individual (i.e. two triplex samples were prepared for each individual, with sample from one of the timepoints spiked into both triplexed samples to use a reference). After labeling, samples for each triplex was combined and desalted and dried again using STAGE tips and the Vacufuge Plus. Peptides were resuspended in 30μl of 0.1% formic acid for liquid chromatography and mass spectrometry analysis (LC-MS). A total of 2 μg per sample was injected into the EasynLC-1000 chromatography system (Thermo) with a 50 cm analytical column, packed in-house with C18, coupled to an Impact II Q-TOF mass spectrometer (Bruker Daltonics, Bremen, Germany), with detailed parameters as previously described47. Data was analysed using MaxQuant (v1.5.5.1) with default values and “Match Between Runs” activated, searched against the human Uniprot database (downloaded on 15 July, 2017).
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:15:59.528.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterQueenie Chan
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue
Instrumentimpact II
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-07-21 07:09:05ID requested
12020-12-01 09:00:14announced
22024-10-22 05:16:01announced2024-10-22: Updated project metadata.
Publication List
10.3389/fimmu.2020.580373;
Ben-Othman R, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aevermann B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Lin DTS, Gladish N, Maclsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kobor MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock REW, Kollmann TR, Sadarangani M, Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults. Front Immunol, 11():580373(2020) [pubmed]
Keyword List
submitter keyword: tissue, blood, systems biology,hepatitis B vaccone
Contact List
Leonard J Foster
contact affiliationBiochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia
contact emailfoster@msl.ubc.ca
lab head
Queenie Chan
contact affiliationDepartment of Biochemistry and Molecular Biology
contact emailqueeniecwt@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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