Rosenthal_Zebrafish_TurboID_P88_SAINT5425_TurboID_injections_2021
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Danio Rerio (ncbitaxon:7955)
SUBMITTER: 
Anne-Claude Gingras
PROVIDER: MSV000087425 | MassIVE | Thu May 13 11:42:00 BST 2021
SECONDARY ACCESSION(S): PXD026007
REPOSITORIES: MassIVE
Similar Datasets
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
Project description:MassIVE title 4: Rosenthal_Zebrafish_TurboID_P88_SAINT5429_miniTurbo_transgenics_2021
SAINT Task ID 5429
This dataset consists of 9 raw MS files and associated peak lists and result files comprising of transgenics (heat-shock) analysis 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:
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Export version: VS4
SAINT Task ID: as listed below
2021-05-14 | MSV000087430 | MassIVE
Project description:MassIVE title 3: Rosenthal_Zebrafish_TurboID_P88_SAINT5428_TurboID_transgenics_2021
SAINT Task ID 5428
This dataset consists of 9 raw MS files and associated peak lists and result files comprising of transgenics (heat-shock) analysis of the TurboID 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: 5428
2021-05-14 | MSV000087429 | MassIVE
Project description:MassIVE title 5 Rosenthal_Zebrafish_TurboID_P88_SAINT5454_TurboID_transgenics_conditions_2021
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This dataset consists of 22 raw MS files and associated peak lists and result files comprising of transgenics (heat-shock) analysis of the TurboID and comparison of conditions (biotin and heat shock timing and concentration).
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: 5454
2021-05-14 | MSV000087431 | MassIVE
Project description:This dataset consists of 6 raw MS files and associated peak lists and result files, acquired on an Orbitrap classic or Orbitrap Velos mass spectrometer operated in Data Dependent Acquisition mode.
Samples were generated by Bernard Liu, formerly of the Pawson lab. MassIVE report was performed by Anne-Claude Gingras. The files are associated with a manuscript submitted for publication by Lucian Tomaz et al. that describes the relocalization of Mutated in Colorectal Cancer (MCC) during intestinal cell differentiation.
Dr. Ray Dunn is the corresponding author of the manuscript (ray.dunn@ntu.edu.sg); Anne-Claude Gingras or Bernard Liu (Bernard.a.liu@gmail.com) should be contacted for questions on this submission (gingras@lunenfeld.ca).
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: P17,
Export version: N/A
SAINT Task ID: 5987
2022-04-14 | MSV000089258 | 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: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:This dataset consists of 31 raw MS files and associated peak lists and result files, acquired on Thermo Velos Orbitrap, Orbitrap Elite and AB SCIEX TripleTOF 6600 mass spectrometers operated in DDA mode. Samples were processed by Zhen-Yuan Lin.
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 36,
SAINT Task ID: 3363
2018-03-25 | MSV000082207 | MassIVE
Project description:This submission contains the mass spectrometry files for the manuscript by Samavarchi-Tehrani et al. that describes the use of lentiviral delivery of BirA*-tagged transgenes into HeLa, BJ and MEF cells or in comparison to stably integrated transgene in Flp-In T-REx HeLa cell lines. This submission contains the human files from a set of 56 raw MS files and associated peak lists and result files, acquired on a TripleTOF 6600 spectrometer (AB SCIEX, Concord, Ontario, Canada) operated in Data Dependent Acquisition mode. Samples were generated by Payman Samavarchi-Tehrani.
This massIVE submission contains the files for the mouse samples. Please see accompanying submission for the human samples.
Raw files are deposited here in MassIVE. For questions, please contact Anne-Claude Gingras (gingras@lunenfeld.ca) or Payman Samavarchi-Tehrani (payman@lunenfeld.ca).
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 112, Export versions VS4 (Viral BioID Benchmark)
SAINT Task ID: Flp-HeLa:3596; HeLa:3139; BJ:3140; MEF:3141
2018-06-01 | MSV000082430 | MassIVE