Data from: Assessment of protein conformation via diazirine-promoted oxidation
Data files
Jan 22, 2026 version files 24.19 GB
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Archive.zip
24.19 GB
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README.md
2.37 KB
Abstract
Photo-affinity labeling (PAL) utilizes photoreactive molecules to derivatize proteins in a solvent-accessible dependent manner. The site and frequency of the products of this reaction can be used to garner insights into the conformation of the protein. In this work, we document and characterize a novel oxidation process instigated by UV irradiation of aromatic diazirines. Diazirine is an increasingly utilized reagent for probing protein conformations, and this labeling has yet to be documented. We initially assess the selectivity of the chemical reaction and find that it is highly selective to methionine (Met) and tryptophan (Trp) residues. We next examine whether this oxidative labeling can be utilized to evaluate protein conformation. We assess native and urea-denatured ubiquitin and cytochrome c, holo- and apo-myoglobin, and native and copper-bound b-2-microglobulin. In all protein systems but ubiquitin, this diazirine-promoted oxidation readily differentiates between the two protein conformations
Dataset DOI: 10.5061/dryad.4qrfj6qrh
Description of the data and file structure
This deposit contains the raw Bruker data files used to generate all figures presented in the manuscript of the same title. We recommend using Bruker DataAnalysis software to view the mass spectra; however, any software capable of processing timsTOF data may be used. Detailed descriptions of the instrumental parameters over the course of the measurements can be found in the Experimental Section of the accompanying manuscript.
Files and variables
File: Archive.zip
Description: Each data field is labeled with the precise figure number that the data was used in. This is an analytical chemistry manuscript focused on technique development, so a handful of standard proteins were assessed. Each data filed indicates if the protein tested was native, denatured, what replicate number and anything else of value. Cu indicates copper bound.
- All MS spectra for Figure 1A-E, 2A, 2D, 3, 4A, 4B, S1, S7A-B, and S8A were obtained by averaging the base peak chromatogram (BPC) over the 0–2 minute time window.
- All MS spectra for Figure S2A-B and S3 were obtained by averaging the base peak chromatogram (BPC) over the 0–1 minute time window.
- The MS/MS spectra for Figure S4, S5, and S6 were obtained by averaging the total ion chromatogram (TIC) over the time windows of 6.5–8.5 minutes, 9.6–11.6 minutes, and 2.6–4.6 minutes, respectively.
- All LC-MS/MS data for Figure 2B, 2E, 4C, S8B, S9, S10, S11, and S12 were manually analyzed by extracting ion chromatograms corresponding to the theoretical m/z values obtained using the MS-Product tool in the Protein Prospector database. (https://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msproduct).
Code/software
We recommend using Bruker DataAnalysis software to view the mass spectra; however, any software capable of processing timsTOF data may be used (e.g., mzmine: https://mzio.io/mzmine-news/). Detailed descriptions of the instrumental parameters over the course of the measurements can be found in the Experimental Section of the accompanying manuscript.