PXD071912

PXD071912 is an original dataset announced via ProteomeXchange.

Title	TurboID bioproximity analysis of Pax3-FOXO1 and Foxo1, Zimmerman and Counter
Description	Samples were spiked with 1 or 2 pmol bovine casein as an internal quality control standard. Next, they were brought to 5% SDS and reduced for 15 min at 80C, alkylated with 20 mM iodoacetamide for 20 min at room temperature, then supplemented with a final concentration of 1.2% phosphoric acid and 396 uL of S-Trap (Protifi) binding buffer (90% MeOH/100mM TEAB) (Table 1). Proteins were trapped on the S-Trap micro cartridge, digested using 1ug sequencing grade trypsin (Promega) for 1 hr at 47C, and eluted using 50 mM TEAB, followed by 0.2% FA, and lastly using 50% ACN/0.2% FA. All samples were then lyophilized to dryness. Samples were resuspended in 40uL of 1% TFA/2% acetonitrile with 12.5 fmol/uL of yeast ADH. A study pool QC (SPQC) was created by combining equal volumes of each sample and run periodically throughout the study. Prior to LC-MS analysis, a florescent peptide level quantitation assay (Thermo) was performed on the SPQC sample and volumetric loading for all samples was adjusted such that a target 300ng of the SPQC was analyzed. Quantitative LC/MS/MS was performed using an EvoSep One UPLC coupled to a Thermo Orbitrap Astral high resolution accurate mass tandem mass spectrometer (Thermo). Briefly, each sample loaded EvoTip was eluted onto a 1.5 um EvoSep 150um ID x 15cm performance (EvoSep) column using the SPD30 gradient at 55C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (m/z 200) full MS scan from m/z 380-980 in the OT with a target AGC value of 4e5 ions. Fixed DIA windows of 4 m/z from m/z 380 to 980 DIA MS/MS scans were acquired in the Astral with a target AGC value of 5e4 and max fill time of 6 ms. HCD collision energy setting of 27% was used for all MS2 scans.
HostingRepository	MassIVE
AnnounceDate	2026-03-26
AnnouncementXML	Submission_2026-03-26_12:06:10.407.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erik Soderblom
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-12 06:54:46	ID requested
⏵ 1	2026-03-26 12:06:11	announced

no publication

submitter keyword: label free, bioid, astral, DatasetType:Proteomics

Christopher Counter
contact affiliation	Duke University Medical Center
contact email	chris.counter@duke.edu
lab head
Erik Soderblom
contact affiliation	Duke University
contact email	es114@duke.edu
dataset submitter

MassIVE dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v11/MSV000100198/