⮝ Full datasets listing
PXD075717
PXD075717 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Loss of ALDH3A1 Drives Adaptive Drug Transporter-Mediated Resistance to Gemcitabine in Pancreatic Cancer |
| Description | LC/MS-MS analysis were performed peptide sample preparation, TMT labeling and high pH reversed-phase fractionation, Mass spectrometry analysis, and proteome search and bioinformatic analysis. Briefly, cell pellet preparation was performed using the S-Trap mini spin column protocol (Protifi, USA). Tryptic peptides (80 ug per sample) were labeled with TMT 6-plex reagents (Thermo Fisher Scientific, USA) following the manufacturer's instructions. Labeling efficiency was validated by LC-MS/MS using 2.5% of each sample. The resulting fractions were vacuum-dried and stored at -80'C until LC-MS/MS analysis. Dissolved samples were analyzed using an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific, USA) coupled to an UltiMate 3000 RSLCnano system (Thermo Fisher Scientific, USA) equipped with a nano electrospray at Korea Basic Science Institute (OC104). Raw MS data were processed as previously described with minor modifications (23). Raw files were converted to mzML using MSConvert (v3.0.20033), and MS2 files were extracted via an in-house Python 3.8 script using the pyOpenMS module (v2.8.0). The human proteome database (UniProt, June 2, 2020) was used with appended reversed sequences and common contaminants. Protein identification was performed using the Integrated Proteomics Pipeline (IP2, v5.1.2) with the following search parameters: 10 ppm precursor tolerance, 100 ppm fragment ion tolerance, minimum peptide length of 6 residues, up to two missed tryptic cleavages, static modifications of +229.1629 Da (TMT) on lysine and N-terminus, +57.02146 Da (carbamidomethylation) on cysteine, and variable oxidation (+15.9949 Da) on methionine. False discovery rates (FDR) were maintained below 1% at the spectral and protein levels using DTASelect. Quantification was performed using Census software based on TMT reporter ion intensities extracted from MS2 spectra. Genes with expression changes greater than 2-fold and p-value < 0.05 were identified as differentially expressed genes (DEGs). |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-03-16 |
| AnnouncementXML | Submission_2026-03-16_22:06:07.824.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Heeyoun Hwang |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | iodoacetamide - site C; Oxidation; TMTpro |
| Instrument | Orbitrap Eclipse |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-03-16 21:46:57 | ID requested | |
| ⏵ 1 | 2026-03-16 22:06:08 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: ALDH3Ai, Pancreatic Cancer, Gemstabine, DatasetType:Proteomics |
Contact List
| Chan Hee Park | |
|---|---|
| contact affiliation | 1 Division of Gastroenterology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine |
| contact email | PARKCH09@yuhs.ac |
| lab head | |
| Heeyoun Hwang | |
| contact affiliation | KBSI |
| contact email | heeyounh@kbsi.re.kr |
| dataset submitter | |
Full Dataset Link List
| 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/MSV000101149/ |
