PXD019680

PXD019680 is an original dataset announced via ProteomeXchange.

Title	Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing
Description	As the SARS-CoV-2 pandemic continues to spread, thousands of scientists around the globe have changed research direction to better understand how the virus works and to find out how it may be tackled. The number of manuscripts on pre-print servers is soaring and peer-reviewed publications using mass spectrometry-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Calu-3, CaCo-2, ACE-A549 and Vero E6 that characterizes their protein expression profile including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the oncogene breast BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein coding regions of the African green monkey genome. Monitoring changes of the proteome upon viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors and proteins involved in innate immunity. The extensive protein and peptide coverage obtained, can also be used to build spectral libraries for setting up data independent acquisition (DIA) or parallel reaction monitoring (PRM) experiments for host or viral proteins. Based on a library of 98 stable isotope labeled synthetic peptides representing 11 viral proteins, we developed PRM assays for nano-flow as well as micro-flow LC-MS/MS. We assessed the merits of these PRM assays by the analysis of supernatants of virus infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained, we critically discuss the merits of mass spectrometry-based proteomics for SARS-CoV-2 research and testing.
HostingRepository	PanoramaPublic
AnnounceDate	2020-09-11
AnnouncementXML	Submission_2020-09-11_12:44:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Christina Ludwig
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Oxidation; Label:13C(6)15N(2); Label:13C(6)15N(4); Label:13C(6)15N(1)
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-09 14:18:20	ID requested
⏵ 1	2020-09-11 12:44:17	announced

Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B, Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Mol Cell Proteomics, 19(9):1503-1522(2020) [pubmed]

submitter keyword: SARS-CoV-2, proteomics, mass spectrometry, stable isotope labeling, parallel reaction monitoring, Vero E6, ACE2, infectome, nasopharyngeal swabs

Christina Ludwig
contact affiliation	Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TU Munich, Freising
contact email	tina.ludwig@tum.de
lab head
Christina Ludwig
contact affiliation	Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TU Munich, Freising
contact email	tina.ludwig@tum.de
dataset submitter

Panorama Public dataset URI