PXD042548
PXD042548 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue |
| Description | This data set contains raw files from the following samples: 1) a simple standard mixture of proteins used for optimization of labeling conditions and 2) human proteoforms extracted from a biopsied prostate tumor sample. Standard proteins are labeled with the natural-isotopic version of a cysteine-specific chemical labeling reagent, dimethyl-leucine hydrazide (DLH) (Modification mass: 213.1479 Da, Modification formula: C10 H19 O2 N3). 3 technical replicates of 3 replicate labeling experiments performed at the optimized labeling conditions are provided. Extracted prostate tumor proteoforms were split into two portions and 1 was labeled with the NeuCode-light DLH isotopologue (Modification mass: 222.15896 Da), and the other was labeled with the NeuCode-heavy DLH isotopologue (222.20422). After labeling, these samples were combined in a 2:1 ratio (NeuCode heavy:NeuCode light). The combined proteoforms were separated into 8 size-based fractions using PEPPI fractionation. The following intact-mass (i.e. LC-MS, no precursor fragmentation) files were collected: Fractions 1-4 were analyzed at MS1 resolutions of 240,000 and 500,000. Fractions 5 and 6 were analyzed at MS1 resolutions of 120,000, 240,000, and 500,000. Fractions 7 and 8 were analyzed at MS1 resolutions of 120,000 and 240,000. This produced 18 intact-mass LC-MS raw files. Each fraction was also analyzed by Top-down mass spectrometry (LC-MS/MS), producing 8 LC-MS/MS raw files. Also included are: 1) a database containing the proteins in the mixture on which labeling optimization was performed 2) a protein-pruned GPTMD database derived from previous BU analysis of prostate tumors used to search the TD and NeuCode intact-mass data 3) the proteoform atlas produced from the collected TD data and used to search the NeuCode intact-mass data. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-09-23 |
| AnnouncementXML | Submission_2024-09-23_11:29:38.182.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | John Pavek |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | unknown modification |
| Instrument | Orbitrap Fusion Lumos; Q Exactive HF |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-05-30 12:30:55 | ID requested | |
| ⏵ 1 | 2024-09-23 11:29:38 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: NeuCode, Chemical Labeling |
Contact List
| Lloyd M. Smith | |
|---|---|
| contact affiliation | University of Wisconsin - Madison |
| contact email | smith@chem.wisc.edu |
| lab head | |
| John Pavek | |
| contact affiliation | UW-Madison |
| contact email | jpavek@wisc.edu |
| 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/v05/MSV000092055/ |
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