PXD036798-1

PXD036798 is an original dataset announced via ProteomeXchange.

Title	SARS-CoV-2 variants evolve convergent strategies to remodel the host response: Affinity Purification Mass Spectrometry (APMS)
Description	We sought to compare differences in the SARS-CoV-2 virus-human protein interaction networks between mutated (from the SARS-CoV-2 variants of concern) and wild-type viral proteins. Here, we ectopically expressed 2x-strep-tagged constructs encoding mutant or wild-type SARS-CoV-2 viral proteins in HEK293T cells followed by affinity purification mass spectrometry (APMS). This allowed us to quantify differences in protein-protein interactions attributable to mutations present within SARS-CoV-2 variant proteins.
HostingRepository	PRIDE
AnnounceDate	2024-02-16
AnnouncementXML	Submission_2024-02-15_19:48:12.489.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mehdi Bouhaddou
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-17 02:55:22	ID requested
⏵ 1	2024-02-15 19:48:13	announced
2	2024-10-22 06:30:48	announced	2024-10-22: Updated project metadata.

10.1016/j.cell.2023.08.026;

Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, H, ü, ttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ, SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell, 186(21):4597-4614.e26(2023) [pubmed]

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: omics, APMS, lung, SARS-CoV-2, host response, host, infection, COVID-19,protein-protein interactions

Nevan J.
contact affiliation	Professor, Department of Cellular and Molecular Pharmacology
contact email	nevan.krogan@ucsf.edu
lab head
Mehdi Bouhaddou
contact affiliation	UCSF
contact email	mehdibouhaddou@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/2024/02/PXD036798

PRIDE project URI

• PRIDE
  1. PXD036798
     1. Label: PRIDE project
     2. Name: SARS-CoV-2 variants evolve convergent strategies to remodel the host response: Affinity Purification Mass Spectrometry (APMS)