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.
[doi:10.25345/C5RN30J3N]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: NeuCode ; Chemical Labeling
Principal Investigators: (in alphabetical order) |
Lloyd M. Smith, University of Wisconsin - Madison, USA |
Submitting User: | jgpavek1217 |
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Owner | Reanalyses | |
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