PXD020474-1

PXD020474 is an original dataset announced via ProteomeXchange.

Title	Systems biology of blood and tissue for comprehensive analysis of immune response to hepatitis B vaccine in adults
Description	Protein 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).
HostingRepository	PRIDE
AnnounceDate	2020-12-01
AnnouncementXML	Submission_2020-12-01_09:00:12.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Queenie Chan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	impact II

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-21 07:09:05	ID requested
⏵ 1	2020-12-01 09:00:14	announced
2	2024-10-22 05:16:01	announced	2024-10-22: Updated project metadata.

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]

submitter keyword: hepatitis B vaccone, systems biology, blood, tissue

Leonard J Foster
contact affiliation	Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia
contact email	foster@msl.ubc.ca
lab head
Queenie Chan
contact affiliation	Department of Biochemistry and Molecular Biology
contact email	queeniecwt@gmail.com
dataset submitter

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/pride/data/archive/2020/12/PXD020474

PRIDE project URI

• PRIDE
  1. PXD020474
     1. Label: PRIDE project
     2. Name: Systems biology of blood and tissue for comprehensive analysis of immune response to hepatitis B vaccine in adults