PXD083806-1

PXD083806 is an original dataset announced via ProteomeXchange.

Title	Alveolar Cytochrome P450 Mediates Butylated Hydroxytoluene-Induced Electrophilic Injury and Apoptosis
Description	Twenty micrograms of cell lysates was adjusted to 5% SDS followed by reduction with 10 mM DTT, alkylation with 25 mM iodoacetamide and trypsin digestion using an S-trap micro device (Protifi). Lyophilized peptides were reconstituted in 80 microliters of 0.1% formic acid. SPQC samples were prepared by mixing equal volumes of all samples. Finally, 3 microliters of samples (including replicates of the SPQC) were loaded onto Evotips, followed by an addition of 50 fmol yeast ADH1 digestion (Waters Massprep). Liquid chromatography tandem mass spectrometry (LC-MS/MS) an Evosep One LC (30 sample-per-day) coupled to a ThermoFisher Orbitrap Astral. The data-independent MS/MS analysis used a 240,000 resolution Orbitrap precursor ion (MS1) scan from 380-1080 m/z, automatic gain control (AGC) target of 500% and maximum injection time (IT) of 50 ms, collected every 0.6 s in centroid mode. MS/MS was performed in the Astral analyzer using a DIA method with default charge state = 3, precursor mass range of 380-980 m/z,4 m/z isolation windows, AGC target of 500%, max IT of 6 ms and a normalized collision energy (NCE) of 28%. Data-dependent analysis used a 240,000 resolution MS1 scan from 375-1500 m/z and was collected every 1 s, followed by a ddMS2 Astral method with intensity threshold of 1E4, auto dynamic exclusion, 1.2 m/z isolation window, stepped collision energy of 24,26,28 %NCE, AGC target of 100%, maximum IT of 20 ms. DIA MS data was converted to *.htrms format using HTRMS converter and processed in Spectronaut 20.5 (Biognosys; 20.5.260227.92449). A spectral library was built using direct-DIA searches of all individual files (DDA + DIA) and used a Uniprot mouse database (UP000000589) downloaded on 04/08/2022 and appended with Cyp2b10 WT, Cyp2b10 C436A and as well as additional contaminant sequences using FragPipe (17,221 total entries). Search settings included trypsin/P specificity with up to 2 missed cleavages and peptide length from 7-52 amino acids with variable acetyl (protein N-term), carbamidomethyl(Cys) and BHT(OH)Cys modification. For DIA analysis, default extraction, calibration, identification, and protein inference settings were used. Data was filtered at a 1% precursor and protein group false discovery rate (q-value). Background imputation was optionally selected in Spectronaut. Local normalization of quantified precursors, and protein roll-up with the MaxLFQ algorithm. Diagnostic ions were also extracted from DIA data using the --extract 217.16, 235.17 option in DIA-NN. A mass-tolerant open search of DDA data was performed in FragPipe v24.0 (MSFragger) using the default Open workflow. The precursor mass window was -150 to +500 Da with delta-mass localization enabled; precursor true tolerance and fragment tolerance were 20 ppm with mass calibration/optimization. Additionally, a labile/offset search (diagnostic-ion-enforced site identification) targeting the BHT-quinone-methide Michael adduct (BHTOH, +234.16199 Da) was searched as a labile mass offset (labile_search_mode = labile; mass_offsets = 0.0/234.16199) restricted to cysteine (restrict_deltamass_to = C), with delta-mass fragment localization enabled (localize_delta_mass = 1; labile b/y ion series) and the delta mass reported as a variable modification. Spectra were required to contain BHT-QM diagnostic oxonium evidence: fragments m/z 217.159240 and 235.169805 at a summed relative intensity >=10% of the base peak (diagnostic_intensity_filter = 0.1).
HostingRepository	MassIVE
AnnounceDate	2026-09-07
AnnouncementXML	Submission_2026-09-07_19:35:54.029.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matt Foster
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Carbamidomethyl; Oxidation; Acetyl; BHTOH
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2026-09-07 17:31:34	ID requested
⏵ 1	2026-09-07 19:35:54	announced

no publication

submitter keyword: BHT, fibrosis, alveoli, DatasetType:Proteomics

Michael T. Forrester
contact affiliation	Duke University
contact email	michael.forrester@duke.edu
lab head
Matt Foster
contact affiliation	Duke University
contact email	mwfoster@duke.edu
dataset submitter

MassIVE dataset URI

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