DOI: 10.5061/dryad.4qrfj6qrh
title: Data from: Assessment of protein conformation via diazirine-promoted oxidation

description: 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
description: # Data from: Assessment of protein conformation via diazirine-promoted
 oxidation Dataset DOI:
 [10.5061/dryad.4qrfj6qrh](https://doi.org/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](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/](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.