PXD028633

PXD028633 is an original dataset announced via ProteomeXchange.

Title	Isolation of mouse and human MHC class I- and II-associated peptides for the analysis of immunopeptidomes by mass spectrometry
Description	Immunopeptidomics is an emerging field that fuels and guides the development of vaccines and immunotherapies. More specifically, it refers to the science of investigating the composition of peptides presented by major histocompatibility complex (MHC) class I and class II molecules using mass spectrometry (MS) technology platforms. Among all the steps in a MS-based immunopeptidomic workflow, sample preparationis critically important for capturing high-quality data of therapeutic relevance. Here, we describe step-by-step instructions to isolate MHC class I and II-associated peptides by immunoaffinity purification from quality control (QC) samples. Our QC samples are MHC class I and class II peptides isolated from mouse (EL4 and A20) and human (JY) cell lines. We thoroughly describe the various reagents and specfic antibodies that are used too isolate MHC-associated peptides from these cell lines, including the steps to verify the beads-binding efficiency of the antibody and the elution efficiency of the MHC-peptide complexes from the beads. QC samples generated using the described protocol can be used to establish and standardize immunopeptidomic workflow, as well as to benchmark new protocols. We anticipate that the visualized protocol provided in this report will represent a great starting point for any non-expert in addition to foster the instra- and inter-laboratory reproducibility of the sample preparation procedure in immunopeptidomics.
HostingRepository	PRIDE
AnnounceDate	2021-12-07
AnnouncementXML	Submission_2021-12-08_05:51:42.381.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD028633
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	isabelle sirois
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-19 22:04:24	ID requested
1	2021-12-07 12:59:49	announced
2	2021-12-08 05:50:51	announced	2021-12-08: Updated publication reference for PubMed record(s): 34798331.
⏵ 3	2021-12-08 05:51:48	announced	2021-12-08: Updated publication reference for PubMed record(s): 34798331. 2021-12-08: Updated publication reference for PubMed record(s): 34798331, 34723952.

Kovalchik KA, Ma Q, Wessling L, Saab F, Duquette JD, Kubiniok P, Hamelin DJ, Faridi P, Li C, Purcell AW, Jang A, Paramithiotis E, Tognetti M, Reiter L, Bruderer R, Lanoix J, Bonneil É, Courcelles M, Thibault P, Caron E, Sirois I, MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets. Mol Cell Proteomics, 21(1):100178(2022) [pubmed]

Sirois I, Isabelle M, Duquette JD, Saab F, Caron E, Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis. J Vis Exp, (176):(2021) [pubmed]

submitter keyword: immunopeptidome, mass spectrometry, MHC class I associated peptides, MHC class II associated peptides, mouse, Human

Etienne Caron
contact affiliation	1CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada 2 Department of Pathology and cellular biology, Faculty of Medicine, Universite de Montreal, QC H3T 1J4, Canada
contact email	Etienne.caron@umontral.ca
lab head
isabelle sirois
contact affiliation	Centre de recherche Hôpital Sainte-Justine
contact email	isabelle.sirois.phd@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/2021/12/PXD028633

PRIDE project URI

• PRIDE
  1. PXD028633
     1. Label: PRIDE project
     2. Name: Isolation of mouse and human MHC class I- and II-associated peptides for the analysis of immunopeptidomes by mass spectrometry