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
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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.
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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.
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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
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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:
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Export version VS15
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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
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Project description:MassIVE title 3: Rosenthal_Zebrafish_TurboID_P88_SAINT5428_TurboID_transgenics_2021
SAINT Task ID 5428
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Each MassIVE submission is associated with 5 Supplementary Files (in addition to this README file)
Table 1 describes the composition of this dataset
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