PXD044965

PXD044965 is an original dataset announced via ProteomeXchange.

Title	ALK signalling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition
Description	Phosphoproteomics DIA LC-MSMS analysis Phospho-enriched peptides were resuspended in aqueous formic acid and 0.2 ug of peptides subjected to LC-MS/MS analysis using an Orbitrap Exploris 480 Mass Spectrometer fitted with an Vanquish Neo (both Thermo Fisher Scientific) and a custom-made column heater set to 60C. Peptides were resolved using a RP-HPLC column (75um x 30cm) packed in-house with C18 resin (ReproSil-Pur C18-AQ, 1.9 um resin; Dr. Maisch GmbH) at a flow rate of 0.2 uLmin-1. Separation of peptides was achieved using the following gradient: 4% Buffer B to 10% Buffer B in 5 min, 10% Buffer B to 35% Buffer B in 45 min, 35% Buffer B to 50% Buffer in 10 min. Buffer A was 0.1% formic acid in water and buffer B was 80% acetonitrile, 0.1% formic acid in water. The mass spectrometer was operated in DIA acquisition mode with a total cycle time not exceeding approximately 3 s. For MS1, the following parameters were set: Resolution: 120,000 FWHM (at 200 m/z), Scan Range: 350-1400 m/z, Injection time: 25 ms, Normalized AGC Target: 300%. MS2 (SWATH) scans were acquired using the following parameters: Isolation Window: 8 m/z, HCD Collision Energy (normalized): 28%, Normalized AGC target: 1000%, Resolution: 15,000 FWHM (at 200 m/z), Precursor Mass Range: 400 - 1200 m/z, Max. Fill Time: 22 ms, DataType: Centroid. In total 100 DIA (MS2) mass windows per MS cycle followed by the one MS1 scan. Data analysis of phosphoproteomics DIA-MS data The acquired raw files were searched using SpectroNaut (v17.1, PTM workflow, default settings) against a human database (consisting of 20360 protein sequences downloaded from Uniprot on 20220222) and 392 commonly observed contaminants using the following search criteria: full tryptic specificity was required (cleavage after lysine or arginine residues, unless followed by proline); 3 missed cleavages were allowed; carbamidomethylation (C) was set as fixed modification; oxidation (M), N-acetlyation (N-term) and phosphorylation (STY) were applied as variable modifications. The normalized, phosphosite centric and statstically analysed quantiative results were exported as a csv-table from the SpectroNaut software using the candidate list export option without any filters applied.
HostingRepository	MassIVE
AnnounceDate	2023-12-13
AnnouncementXML	Submission_2023-12-13_02:41:55.305.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alex Schmidt
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Phospho
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-30 06:45:37	ID requested
⏵ 1	2023-12-13 02:41:55	announced

no publication

submitter keyword: alk, signalling

Ruth Palmer
contact affiliation	University of Gothenburg
contact email	ruth.palmer@gu.se
lab head
Alexander Schmidt
contact affiliation	Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland
contact email	alex.schmidt@unibas.ch
lab head
Alex Schmidt
contact affiliation	University of Basel
contact email	alex.schmidt@unibas.ch
dataset submitter

MassIVE dataset URI

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