PXD073882

PXD073882 is an original dataset announced via ProteomeXchange.

Title	Low-input, proteomic analysis of Caecomyces churrovis hydrogenosomes
Description	We performed enzyme assays with fractions (#1-8) collected after OptiPrep density gradient centrifugation. The fractions with high malic enzyme activity (NADP+) (#4, 5, 6) were pooled and processed as one sample. In total three replicates of independently prepared fractions were used for nanoPOTS analysis as described below. [LC-MS analysis]: For mass spectrometry analysis, a Bruker timsTOF-SCP with a Captive Spray source was coupled to our in-house nanoPOTS autosampler. The timsTOF-SCP was operated in high-sensitivity, DDA-PASEF mode with a duty cycle of 1.56 s consisting of 8 PASEF MS/MS scans from 100 to 1700 m/z with an ion mobility range (1/K0) from 0.6 to 1.6 Vs/cm2. Capillary voltage was set to 1500 V. The TIMS ramp and accumulation time were set to 166 ms while the collision energy was ramped linearly as a function of mobility from 59ev at 1/K0 = 1.6 Vs/cm2 to 20 eV at 1/K0 = 0.6 Vs/cm2. Precursors with charge state from 0 to 5 were selected with a target value of 10,000 and intensity threshold of 500. Isolation width was set to 2 m/z at or below 700 m/z and 3 m/z at or above 800 m/z, with a linear interpolation between the two points. Isolated precursors were excluded from analysis for 0.4 min after isolation. [Data Analysis]: All Bruker proteomic .D files were processed by FragPipe (version 20.0) and searched against C. churrovis protein sequence database (14,772 protein entries) acquired from the Joint Genome Institute. These databases included target sequences as well as decoy sequences and common protein contaminants. MSfragger version 3.8, IonQuant version 1.9.8, and Philosopher version 5.0.0 were applied to the search. Search settings included a precursor mass tolerance of +/- 20 ppm, fragment mass tolerance of +/- 20 ppm, deisotoping, trypsin enzyme specificity, carbamidomethylation as a fixed modification, and several variable modifications (oxidation of methionine, N-terminal acetylation, and pyro-glutamate). Protein and peptide identifications were filtered to a false discovery rate of less than 1% within FragPipe. IonQuant match-between-runs (MBR) was set to "TRUE" and an MBR false discovery rate of 1% at ion level was used to reduce false positive matches. Peptide abundances were rolled up to protein abundances using a top N strategy and median normalization across runs was performed within FragPipe.
HostingRepository	MassIVE
AnnounceDate	2026-07-29
AnnouncementXML	Submission_2026-07-29_15:32:48.733.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Monroe
SpeciesList	scientific name: Caecomyces churrovis; NCBI TaxID: 2019372;
ModificationList	Oxidation; Carbamidomethyl; Acetyl
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-31 19:59:48	ID requested
⏵ 1	2026-07-29 15:32:49	announced

no publication

submitter keyword: anaerobic fungi, nanoPOTS, microPOTS, hydrogenosomes, DatasetType:Proteomics

Scott E. Baker
contact affiliation	Pacific Northwest National Laboratory
contact email	scott.baker@pnnl.gov
lab head
Matthew Monroe
contact affiliation	Pacific Northwest National Laboratory
contact email	matthew.monroe@pnnl.gov
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/v12/MSV000100685/