Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted multiplexed proteomics of SARS-CoV-2 peptides in ALI cells

ABSTRACT: Human air-liquid-interface cultured cells (ALI) were infected with SARS-CoV-2 in presence or absence of the drug aprotinin. Targeted proteomics were performed on previously identified peptides modified with TMTpro.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: Kevin Klann

LAB HEAD: Christian Münch

PROVIDER: PXD019950 | Pride | 2020-11-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20200621_KKL_CoV2_Targeted_MS2_new-1.msf	Msf
	20200621_KKL_CoV2_Targeted_MS2_new.raw	Raw
	Mass_list_02.txt	Txt

Items per page:

1 - 3 of 3

Publications

Aprotinin Inhibits SARS-CoV-2 Replication.

Bojkova Denisa D Bechtel Marco M McLaughlin Katie-May KM McGreig Jake E JE Klann Kevin K Bellinghausen Carla C Rohde Gernot G Jonigk Danny D Braubach Peter P Ciesek Sandra S Münch Christian C Wass Mark N MN Michaelis Martin M Cinatl Jindrich J

Cells 20201030 11

Severe acute respiratory syndrome virus 2 (SARS-CoV-2) is the cause of the current coronavirus disease 19 (COVID-19) pandemic. Protease inhibitors are under consideration as virus entry inhibitors that prevent the cleavage of the coronavirus spike (S) protein by cellular proteases. Herein, we showed that the protease inhibitor aprotinin (but not the protease inhibitor SERPINA1/alpha-1 antitrypsin) inhibited SARS-CoV-2 replication in therapeutically achievable concentrations. An analysis of prote ...[more]

PMID: 33143316

Similar Datasets

HEK293T cell translatome analysis upon Torin1 treatment or single amino acid withdrawal. Related to Supplementary Table 6 from An et al (2020)

Project description:HEK293T subject to Single AA starvation dataset and translatome analysis was determined using Azidohomoalanine (AHA) incorportation, Biotin-click, and streptavidin enrichment. TMTpro 16plex labels was used.

2020-04-30 | PXD017861 | Pride

scRNA-seq of canalicular stage human fetal lung cultured under air-liquid interface

Project description:Small pieces (<0.5 cm of diameter) were isolated from distal regions of 125 day male human fetal lung and cultured on floating poly-carbonate membranes on top of serum and growth factor free medium under air-liquid interface conditons (ALI). ALI explants underwent changes in gene expression indicative of alveolar epithelial cell differentiation under these conditions. scRNA-sequencing was performed on fetal tissue prior to culture (day 0) and day 3, 6, 9 and 12 of ALI explant culture.

2023-06-15 | E-MTAB-12959 | biostudies-arrayexpress

HEK293T cell degradome (pulse chase) time course (5h, 10, 15h) analysis upon Torin1 treatment. Related to Supplementary Table 3 from An et al (2020)

Project description:HEK293T Azidohomoalanine (AHA) Pulse Chase (degradome) time course experiment, were cells from various genetic background (WT, ATG7-/-, RB1CC1-/-) are treated or not with Torin1 for 5h, 10h or 15h. Samples are Biotin-click, and streptavidin enriched, digested and labeled with TMTpro 16plex.

2020-04-30 | PXD018158 | Pride

Inhibition of growth factor signaling prevents SARS-CoV-2 replication

Project description:Caco-2 cells were mock-infected or infected with SARS-CoV-2 patient isolates (in biological quintruplicates) for one hour, washed, and incubated for 24 hours before cell harvest. Extracted proteins were digested and split to 1) carry out whole-cell proteomics of a tandem mass tag (TMT) 10-plex samples using liquid chromatography synchronous precursor selection mass spectromety (LC-SPS-MS3), or 2) use Fe-NTA phosphopeptide enrichment (achieving 98% enrichment) for phospho proteome analyses of a TMT 10-plex analyzed by LC-MS2 First 5 channels = control Last 5 channels = infected

2020-05-15 | PXD018357 | Pride

Detection of known and novel small proteins in Pseudomonas stutzeri using a combination of bottom-up and top-down proteomics and proteogenomics

Project description:Here we performed a comprehensive genomic and proteomics analysis of P. stutzeri in aerobic and oxygen-limiting conditions. We combined de novo genome assembly relying on 3rd generation long read sequencing technologies to report the first complete P. stutzeri ATCC14405 genome, which added over 110 kb of sequence and contains 126 full length CDS that were only partially covered in the fragmented short read-based genome assembly available for this strain. With this optimal basis for downstream functional genomics, we next carried out state of the art bottom-up and top-down proteomics analyses to report the most detailed study of proteome remodeling in response to oxygen limitation in P. stutzeri. We identified more than 2900 proteins, i.e. greater than 70% of the theoretical proteome, including 160 annotated small proteins. The proteins included well-established enzymes involved in denitrification and metabolic adaptation to oxygen-limiting conditions, as well as uncharacterized proteins. Notably, we identified 16 novel small proteins that had so far been missed in the genome annotation.

2023-08-04 | PXD037914 | Pride

Proteomic landscape of SARS-CoV-2- and MERS-CoV-infected primary human renal epithelial cells

Project description:Acute kidney injury is strongly associated with mortality in COVID-19 patients. However, host cell changes underlying infection of kidney cells with SARS-CoV-2 remain unknown and prevent understanding of the mechanisms leading to renal pathology. Here, we carried out extensive, dual-level proteomic analyses of primary human kidney cells infected with SARS-CoV-2 or MERS-CoV to disseminate virus and cell type specific changes. We established cellular infection models of proximal and distal tubular epithelial cells derived from human donors. Infected cells were analyzed by quantitative translatome and whole-cell proteomics over time. Our findings reveal shared pathways modified upon infection with both viruses, as well as SARS-CoV-2 specific host cell modulation driving key changes in innate immune activation, cellular protein quality control and mitochondrial biology. In addition, we identified extensive modulation in pathways associated with kidney failure that were instinctively regulated in a virus- and cell type-specific manner. Our findings provide an overview of the effects of SARS-CoV-2 or MERS-CoV infection on primary kidney cells revealing key pathways and highlighting potential treatment options.

2022-01-30 | PXD024398 | Pride

Transcriptome analysis during the time course of regeneration of the human airway mucociliary epithelium

Project description:The regeneration of the airway mucociliary epithelium involves several sequential events including migration, proliferation, polarization and final differentiation (i.e ciliogenesis). We used microarrays to detail the global programme of gene expression that occurs during regeneration and ciliogenesis of the human airway mucociliary epithelium. The four time points of regeneration of the airway epithelium (ALI-D0 which corresponds to the end of proliferation step; ALI-D7 which corresponds to the polarization step; ALI-D14 which corresponds to the onset of ciliogenesis and ALI-D21 corresponding to the terminal differentiation step) for RNA extraction and hybridization on Affymetrix microarrays.

2011-06-06 | E-GEOD-22142 | biostudies-arrayexpress

Phosphoproteomics of human MV4-11 AML cells treated with Gilteritinib

Project description:Internal tandem duplications (ITD) in the receptor tyrosine kinase FLT3 occur in 25% of acute myeloid leukemia (AML) patients and lead to constitutive activation of FLT3, driving leukemia cell survival and proliferation. Quizartinib, crenolanib and gilteritinib are second-generation FLT3 inhibitors (FLT3i) in phase III trials or clinical use for the targeted treatment of FLT3-ITD+ AML. However, they demonstrated only limited benefit and were not curative. A full understanding of cellular resistance factors contributing to this poor response is lacking. Here, we examined cell-autonomous pathways modulated by FLT3i using global translatome and phosphoproteome proteomics to identify non-genetic resistance mechanisms.

2022-08-25 | PXD023123 | Pride

Phosphoproteomics of primary human FLT3-ITD+ AML cells treated with gilteritinib

Project description:Primary human AML cells (newly diagnosed, prior to treatment initation) were obtained from donor after consent and AML blasts were isolated by standard Ficoll centrifugation. AML blasts were treated with FLT3 inhibitor gilteritinib (or DMSO vehicle control) at 10 nM concentration for 6 h, followed by harvest for LC/MS.

2022-08-25 | PXD034080 | Pride

PAM complex sequesters from TIM translocon and becomes part of an insoluble protein fraction under protein folding stress

Project description:Upon mitochondrial dysfunction, mitophagy has been described to be activated by a breakdown of membrane potential leading to PINK1 accumulation on the outer membrane and engulfment of mitochondria for degradation. However, recent findings have indicated that mitophagy may also be triggered in the absence of membrane potential alterations. Here, we report mechanistic details on how inhibition of protein import induces mitophagy independent of mitochondrial membrane depolarization. Carrying out a genome-wide CRISPR/Cas9 screen for regulators of mitophagy, we found that the pre-sequence translocase-associated motor complex PAM controls mitophagy induction. Loss of PAM caused defects in protein import and was sufficient to induce mitophagy without depolarization. Quantitative interaction and aggregation proteomics revealed that PAM was highly sensitive to proteostasis perturbation; upon misfolding conditions, PAM dissociated from the import machinery, sequestered into the insoluble fraction and caused mitophagy despite an intact membrane potential. Our findings extend the current mitophagy model and provide mechanistic insight into how proteostasis perturbation leads to mitophagy induction. They reveal the PAM complex as key folding sensor integrating proteostasis, import and mitophagy.

2022-09-03 | PXD022524 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data