PXD050448

PXD050448 is an original dataset announced via ProteomeXchange.

Title	Targeting ERK-eIF4E Protein Translational Signaling in an Inflammatory Breast Cancer Model of Acquired Resistance and Reversal with an Altered Profile of Ribosomal Proteins Associated with Pathological Complete Response in Patients
Description	Monolayer cells were lysed with RIPA buffer followed by a BCA assay. 25 micrograms of protein was normalized with 5% SDS (w/v) in TEAB, pH 8.5 reduction with 10 mM DTT at 80 degC for 15 min and alkylation with with 25 mM IAM ifor 30 min. SDS was removed, and samples were digested with 1:15 of Sequencing Grade Modified Trypsin (Promega) using an S-trap micro device (Protifi) at 47 degC for 1 h. Peptides were lyophilized, and equal volumes of reconstituted samples were mixed to generate a study pool quality control (SPQC) sample. 1D-LC-MS/MS was performed 0.75 micrograms of each sample in a block-randomized order as described in metadata. Samples were analyzed using a M-Class UPLC system (Waters) coupled to a coupled to a Fusion Lumos mass spectrometer (Thermo) via a Nanospray Flex ionization source. Samples were first trapped on a Symmetry C18 180 micrometer x 20 mm trapping column (5 microliters/min at 99.9/0.1 v/v H2O/MeCN) followed by an analytical sepa-ration using a 1.7 micrometer ACQUITY HSS T3 C18 75 micrometer x 250 mm column (Waters) with a 90 min gradient of 5 to 30% MeCN with 0.1% formic acid at a flow rate of 400 nl/min and column temperature of 55 degC. MS data was collected using BoxCar dataindependent acquisition (BoxCarDIA) with variable window BoxCar and DIA scans defined based on scouting runs. Each cycle utilized a full scan with 120,000 resolution from m/z 400 to 1200 with a normalized AGC target of 300% and 50 ms injection time (IT), two BoxCar scans at 120K resolution with 10 windows each, 100% AGC and auto IT, and a 23 window variable window DIA scan with 30K resolution, AGC target of 1000%, a 60 ms IT and NCE of 33. All data was collected in centroid mode.
HostingRepository	MassIVE
AnnounceDate	2024-03-07
AnnouncementXML	Submission_2024-03-07_11:57:32.137.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matt Foster
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Acetyl
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-07 08:57:06	ID requested
⏵ 1	2024-03-07 11:57:32	announced

no publication

submitter keyword: BoxCar DIA, triple negative, data-independent acquisition

Gayathri Devi
contact affiliation	Duke University
contact email	gayathri.devi@duke.edu
lab head
Matt Foster
contact affiliation	Duke University
contact email	mwfoster@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.ucsd.edu/v07/MSV000094251/