Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rosenthal_Zebrafish_TurboID_P88_SAINT5427_miniTurbo_injections_2021

ABSTRACT: 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

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Danio Rerio (ncbitaxon:7955)

SUBMITTER: Anne-Claude Gingras

PROVIDER: MSV000087428 | MassIVE | Fri May 14 09:15:00 BST 2021

SECONDARY ACCESSION(S): PXD026021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Rosenthal_Zebrafish_TurboID_P88_SAINT5425_TurboID_injections_2021

Project description:Rosenthal MassIVE deposition 1: Rosenthal_Zebrafish_TurboID_P88_SAINT5425_TurboID_injections_2021 SAINT Task ID 5425 This dataset consists of 14 raw MS files and associated peak lists and result files comprising of mRNA injections of the TurboID fused baits. 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: 5425

2021-05-13 | MSV000087425 | MassIVE

Rosenthal_Zebrafish_TurboID_P88_SAINT5429_miniTurbo_transgenics_2021

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: Project: P88 Export version: VS4 SAINT Task ID: as listed below

2021-05-14 | MSV000087430 | MassIVE

Rosenthal_Zebrafish_TurboID_P88_SAINT5428_TurboID_transgenics_2021

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

Rosenthal_Zebrafish_TurboID_P88_SAINT5454_TurboID_transgenics_conditions_2021

Project description:MassIVE title 5 Rosenthal_Zebrafish_TurboID_P88_SAINT5454_TurboID_transgenics_conditions_2021 SAINT Task ID 5454 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

MCC_interactome_centrosome_Tomaz_Dunn

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

Alerasool_Transcription_Factors_P77_VS18_BioID

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

Alerasool_Transcription_Activators_P77_VS17_APMS

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

SamavarchiTehrani_P112_VS4_Viral_BioID_Benchmark_mouse

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 mouse 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 | MSV000082429 | MassIVE

SamavarchiTehrani_P112_VS4_Viral_BioID_Benchmark_human

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

Noordermeer_Shieldin_2018

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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