Piette_Hsp70-JPD_P77_VS7_VS16_APMS_DDA
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TripleTOF 5600
ORGANISM(S): Human Adenovirus 5 (ncbitaxon:28285) Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Anne-Claude Gingras
PROVIDER: MSV000086725 | MassIVE | Tue Jan 19 21:56:00 GMT 2021
SECONDARY ACCESSION(S): PXD023673
REPOSITORIES: MassIVE
Similar Datasets
Project description:This dataset consists of 279 raw MS files and associated peak lists and result files, acquired on a TripleTOF 5600 mass spectrometer operated in Data Dependent Acquisition mode.
DDA files were used for library generation using MSPLIT-DIA and MSGFDB (see details below), but this deposition lists the identification and SAINT scoring using iProphet. The files are associated with a manuscript in press in Molecular Cell by Piette et al. that determines the protein-protein and proximity interaction landscape of every human Hsp70 and J-Domain Protein. Five separate MassIVE submissions are associated with this dataset.
Please see "README" file for details.
2021-01-20 | MSV000086738 | MassIVE
Project description:This dataset consists of 208 raw MS files, acquired on TripleTOF 5600 mass spectrometer operated in Data Independent Acquisition mode. Identification was through MSPLIT-DIA, using a sample-specific library created in MSGFDB; gene mapping was through ProHits 4.0, and SAINTexpress was used for defining proximal interactions (spectral count model). The files are associated with a manuscript in Molecular Cell by Piette et al. that determines the protein-protein and proximity interaction landscape of every human Hsp70 and J-Domain Protein. Five separate MassIVE submissions are associated with this dataset.
2021-01-20 | MSV000086730 | MassIVE
Project description:This dataset consists of 195 raw MS files, acquired on TripleTOF5600 mass spectrometer operated in Data Independent Acquisition mode. The files are associated with a manuscript in Molecular Cell by Piette et al. that determines the protein-protein and proximity interaction landscape of every human Hsp70 and J-Domain Protein. Five separate MassIVE submissions are associated with this dataset. Please see README file for details.
2021-01-20 | MSV000086728 | MassIVE
Project description:This dataset consists of 58 raw MS files and associated peak lists and result files, acquired on a TripleTOF 5600 mass spectrometer operated in Data Dependent Acquisition mode. DDA files were searched through Mascot and Comet, and this deposition lists the identification and SAINT scoring using iProphet.The files are associated with a manuscript submitted for publication by Alerasool et al. that determines the protein-protein and proximity interaction landscape of a subset of transcription factors.
Two separate MassIVE submissions are associated with this dataset: A submission for the AP-MS data a submission for the BioID one.
Contributors: Samples were generated by Nader Alerasool and affinity purification and mass spectrometry was performed by Zhen-Yuan Lin with oversight from Brett Larsen and Anne-Claude Gingras. Analysis was performed by Anne-Claude Gingras, Mikko Taipale and Benjamin L. Piette. Corresponding author: Mikko Taipale (mikko.taipale@utoronto.ca). Anne-Claude Gingras (gingras@lunenfeld.ca) should be contacted for questions on this dataset
Supplementary files and tracking information: This submission is associated with 3 Supplementary Files (in addition to the README file)
Table 1 describes the composition of this dataset
Table 2 lists all the peptide identification evidence (as per iProphet)
Table 3 lists the SAINTexpress interactions
Internal reference from the Gingras lab ProHits implementation:
Project: P77,
Export version: VS18
SAINT Task ID: 5215
2021-05-13 | MSV000087424 | MassIVE
Project description:This dataset consists of 57 raw MS files and associated peak lists and result files, acquired on a TripleTOF 5600 mass spectrometer operated in Data Dependent Acquisition mode.
DDA files were searched through Mascot and Comet, and this deposition lists the identification and SAINT scoring using iProphet.
The files are associated with a manuscript submitted for publication by Alerasool et al. that determines the protein-protein and proximity interaction landscape of a subset of transcription factors.
Two separate MassIVE submissions are associated with this dataset, one for the BioID dataset and this one for the AP-MS data.
Contributors
Samples were generated by Nader Alerasool and affinity purification and mass spectrometry was performed by Zhen-Yuan Lin with oversight from Brett Larsen and Anne-Claude Gingras. Analysis was performed by Anne-Claude Gingras, Mikko Taipale and Benjamin L. Piette.
Corresponding author: Mikko Taipale (mikko.taipale@utoronto.ca). Anne-Claude Gingras (gingras@lunenfeld.ca) should be contacted for questions on this dataset
Supplementary files and tracking information
This submission is associated with 3 Supplementary Files (in addition to this README file)
Table 1 describes the composition of this dataset
Table 2 lists all the peptide identification evidence (as per iProphet)
Table 3 lists the SAINTexpress interactions
Internal reference from the Gingras lab ProHits implementation:
Project: P77,
Export version: VS17
SAINT Task ID: 5216
2021-05-12 | MSV000087413 | MassIVE
Project description:HSP70 of grass carp and outer capsid protein VP7 of GCRV determines the early stage of viral entry. Multi-transcriptomic analysis identified HSP70 as a key player in the pathogenesis of GCRV infection. Temperature-dependent, and primarily plasma membrane anchored HSP70 interacts with VP7 to facilitate viral entry during the early phase of GCRV infection. We indentified the interaction of vp7 and hsp70 by MS.
2023-05-09 | PXD036008 | Pride
Project description:This dataset consists of 363 raw MS files and associated peak lists and result files, acquired on a TripleTOF 6600 mass spectrometer operated in Data Independent Acquisition mode (SWATH). It also includes the sequence database used for analysis and the MSPLIT spectral library which was generated from paired samples acquired in Data Dependent Acquisition (DDA) mode.
All sample generation, streptavidin affinity purification, mass spectrometric acquisition, and data analysis was performed by B. Raktan Ahmed.
The files are associated with a manuscript submitted for publication by Dyakov et al. that provides a spatial map of nuclear body-associated proteins with a focus on the paraspeckle and nuclear speckle.
Anne-Claude Gingras is the corresponding author of the manuscript and should be contacted for questions about this dataset (gingras@lunenfeld.ca).
This submission is associated with 4 Supplementary Files (in addition to this README file):
Table 1 describes the composition of this dataset
Table 2 lists the protein evidence for the entire dataset
Table 3 lists the SAINT output (results)
Internal reference from the Gingras lab ProHits implementation:
Project: P131
Export version VS15
SAINT Task ID: 6779
2024-03-12 | MSV000094294 | MassIVE
Project description:Atrial fibrillation (AF) is a major risk factor for cardioembolic stroke. Anticoagulant drugs are effective in preventing AF-related stroke. However, the high frequency of anticoagulant-associated major bleeding is a major concern particularly when antiplatelet treatment is simultaneously administered. Here, microarray analysis in peripheral blood cells in eight patients with AF and stroke and eight AF subjects without stroke identified a stroke related gene expression pattern. HSPA1B, which encodes for heat-shock protein 70 kDa (Hsp70), was the most differentially expressed gene. This gene was downregulated in stroke subjects, a finding confirmed further in an independent AF cohort of 200 individuals. Hsp70 knock-out (KO) mice subjected to different thrombotic challenges developed thrombosis significantly earlier than their wild-type (WT) counterparts. In WT mice, Hsp70 inducers (TRC051384, or tubastatin A) delayed thrombus formation. Remarkably, Hsp70 inducers did not increase the bleeding risk even when aspirin was concomitantly administered. Hsp70 induction was associated with an increased vascular thrombomodulin expression, higher circulating levels of activated protein C (APC) upon thrombotic stimulus and increased protection against endothelial apoptosis. Thus, Hsp70 induction is a novel approach to delay thrombus formation with minimal bleeding risk, being especially promising in situations where there is a major bleeding hazard. Microarray analysis in peripheral blood cells includes eight patients with AF and stroke and eight AF subjects without stroke
2016-04-01 | E-GEOD-66724 | biostudies-arrayexpress
Project description:The major heat shock protein Hsp70 has been shown to form a complex with a scaffold protein Bag3, linking it to multiple signaling pathways. Via these interactions, the Hsp70-Bag3 module functions as a proteotoxicity sensor that controls cell signaling. Here, as a tool to identify signaling pathways regulated by this complex, we utilized JG-98, an allosteric inhibitor of Hsp70 that blocks its interaction with Bag3. Gene expression profiling followed by the pathway analysis indicated that a set of signaling pathways including the unfolded protein response (UPR) was activated by JG-98. Surprisingly, only the translation initiation factor eIF2a-associated branch of the UPR was activated under these conditions, while other UPR branches mediating induction of ER chaperones were not induced, suggesting that the response was not related to ER proteotoxicity and thus to ER-associated kinase PERK1. Indeed, induction of the UPR genes under these conditions was dependent on activation of a distinct cytoplasmic eIF2a kinase, HRI. We demonstrated that the Hsp70-Bag3 complex directly interacted with HRI and regulated phosphorylation of eIF2a upon induction of cytoplasmic proteotoxicity. Therefore, we uncovered a novel signaling response, which regulates cell death upon the buildup of abnormal protein species in cytoplasm via an Hsp70-Bag3-HRI-eIF2a axis.
2021-04-14 | GSE171440 | GEO
Project description:MassIVE title 2: Rosenthal_Zebrafish_TurboID_P88_SAINT5427_miniTurbo_injections_2021
SAINT Task ID 5427
This dataset consists of 13 raw MS files and associated peak lists and result files comprising of mRNA injections of the miniTurbo fused baits.
This README file is associated with five separate MassIVE submissions. All samples were acquired on a Thermo Scientific Orbitrap Fusion mass spectrometer operated in Data Dependent Acquisition mode. All samples were prepared and analyzed by Shimon Rosenthal. The files are associated with a manuscript by Rosenthal et al. that establishes protocols for proximity-dependent biotinylation in zebrafish.
Anne-Claude Gingras and Ian Scott are the corresponding authors of the manuscript (gingras@lunenfeld.ca; ian.scott@sickkids.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca).
Each MassIVE submission is associated with 5 Supplementary Files (in addition to this README file)
Table 1 describes the composition of this dataset
Table 2 lists all the peptide identification evidence (as per iProphet)
Table 3 lists the SAINTexpress interactions
Internal reference from the Gingras lab ProHits implementation:
Project: P88
Export version: VS4
SAINT Task ID: 5427
2021-05-14 | MSV000087428 | MassIVE