PXD058842
PXD058842 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Resistance to anti-EGFR targeted therapy in head and neck squamous cell carcinoma |
| Description | Total proteins were extracted in triplicate from cetuximab-sensitive and -resistant SC263 and SCC22b HNSCC cells. The LC system was coupled to a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Fisher Scientific) programmed to acquire in data-dependent mode. A target of 1.7 x103 ions and a maximum injection time of 80 ms were used for MS/MS. The method was set to analyze the top 20 most intense ions from the survey scan and dynamic exclusion was enabled for 20 s. Tandem mass spectra were processed using MaxQuant software version 1.6.7.0. Proteins were identified using the Andromeda search engine and using the Homo sapiens proteome reference database (UniProt, release 20200130, 20366 entries). The parameters chosen for the identification include: digestion enzyme used was trypsin, maximum number of allowed missed cleavages was two. Oxidation of methionine, N-terminal acetylation, and phosphorylation of serine, threonine and tyrosine were set as variable modifications, while carbamidomethylation of cysteine was set as a fixed modification. A maximum number of 5 modifications per peptide was set. The precursor mass tolerance was set to 4.5 ppm and the fragmentation mass tolerance to 20 ppm. The peptide-to-spectrum match (PSM) and protein false discovery rates (FDR) were set at 1%. The match-between-runs and the label-free quantification (LFQ) methods were enabled using default parameters. After data treatment using MaxQuant, statistical analysis was done using Perseus software (version 1.6.7.0). The data matrix was filtered by removing the potential contaminants and decoy reverse sequences. The LFQ intensities were then log2-transformed and missing values were replaced by imputation based on the normal distribution. This resulted in the quantification of the expression of 2,741 unique proteins. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-12-13 |
| AnnouncementXML | Submission_2024-12-13_01:15:02.221.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | An Wouters |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | instrument model |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-12-13 01:03:54 | ID requested | |
| ⏵ 1 | 2024-12-13 01:15:02 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: head and neck cancer cell lines, LC/MS/MS, resistance to anti-EGFR targeted therapy, DatasetType:Proteomics |
Contact List
| An Wouters | |
|---|---|
| contact affiliation | University of Antwerp |
| contact email | an.wouters@uantwerpen.be |
| lab head | |
| An Wouters | |
| contact affiliation | University of Antwerp |
| contact email | an.wouters@uantwerpen.be |
| 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.ucsd.edu/v07/MSV000096655/ |
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