Dataset DOI: 10.5061/dryad.vq83bk46d

Description of the data and file structure

The following data are the raw, extracted, and processed mass spectrometric data for both pulse-labeling and continuous-labeling HDX-MS experiments of the SARS-CoV-2 spike protein. 

Files and variables

File: Raw_MassSpec_Data_ForPaper_Upload.zip

Description: All .raw files from mass spectra runs for all data presented in the paper. CSV peptide lists generated from tandem MS runs of undeuterated samples by Byonic. This can be read in the open source OpenMS software package. Processed and curated HDExaminer files for all continuous labeling and kinetics experiments can be accessed by contacting the author (not included because of no alternative open source for .HDX files).

File: Kinetics_4C_FracPrefusion_Values.xlsx

Description: Compiled calculated fraction prefusion for 4 peptides from each protein construct during 4 C incubation measured by pulse-labeling soluble or membrane bound SARS-CoV-2 spike with deuterium to quantify the fraction of the population that is prefusion vs open-interface trimer.

Variables

• Condition - construct name
• Residue Start - number of residue at the beginning of peptide
• Residue End - number of residue at the end of the peptide
• Sequence - amino acid sequence of the peptide
• Incubation time at 4C - hours
• Fraction prefusion - Between 0 and 1 - determined from fitting

File: Supplemental_ChicletPlotData.zip

Description: csv files of heatmap (Chiclet Plot) data that are in the supplement of the paper. The plots include data for all high quality peptides identified in the pulse-labeling experiments of SARS-CoV-2 spike protein constructs during 4C incubation. Note that the peptide residue numbers are offset by 28 due to a tag that was included in the FASTA sequence during analysis.

Variables

• Peptide ID - Number of peptide
• Protein - name of protein
• Start - number of first residue in peptide
• End - number of the last residue in peptide
• Sequence - amino acid sequence of peptide
• %D - 1s - Fraction deuterated at beginning of time course
• %D - Xh - Fraction deuterated at the corresponding time.

File: WoodsPlots_Figures_Data.zip

Description: Processed data for the difference woods plots shown in the main text of the paper. Note that the peptide residue numbers are offset by 28 due to a tag that was included in the FASTA sequence during analysis.

Variables:

• Protein - protein construct name
• Start - residue number of the first residue in the peptide
• End - residue number of the last residue in the peptide
• Construct 1 minus Construct 2 - XXXs - Change in deuteration between two constructs at the designated timepoint

File: HDX_ContiunousLabeling_AllResultsTables.zip

Description: Tables of deuteration values for all peptides for each replicate of the continuous labeling experiments in the paper. Note that the peptide residue numbers are offset by 28 due to a tag that was included in the FASTA sequence during analysis.

Variables:

• Protein State - name of protein construct
• Deut Time - time exposed to deuterated buffer
• Experiment - file name where data point comes from
• Start - residue number of the first residue in the peptide
• End - residue number of the last residue in the peptide
• Sequence - amino acid sequence of peptide
• Charge - charge state of peptide in the mass spec data
• Search RT - retention time that peptide was searched at (minutes)
• Actual RT - retention time range that peptide was found at and integrated at
• #Spectra - number of scans for this peptide at this timepoint
• Peak Width - width of m/z isotope peak
• m/z shift - deviation between expected m/z and found m/z
• Max Inty - maximum intensity of an isotope in this peptide
• Exp Cent - Centroid of peptide spectra
• Exp Cent 2 - if bimodal, the centroid of the more deuterated distribution
• Theor Cent - Centroid of the fitted distribution
• Theor Cent 2 - if bimodal, the centroid of the fitted more deuterated distribution
• Score - quality of the spectra and fit (scale of 0-1)
• Cent Diff - not applicable
• #Deut - number of added deuterons to the peptide
• Deut % - percent of exchangeable amides exchanged expressed as a fraction (0-1)
• Cent Diff 2 - not applicable
• #Deut 2 - if bimodal, number of added deuterons to the heavier distribution of the spectra
• Deut % - if bimodal, percent of exchangeable amides exchanged expressed as a fraction (0-1) of the heavier distribution of the spectra
• Confidence - confidence of the data (low, medium, high)

File: 4C_Kinetics_Spectra_Data.zip

Description: CSVs of the extracted mass spectra for all timepoints of all peptides for all replicates used to calculate the rate of interconversion from the prefusion conformation to the open-interface trimer conformation during incubation at 4C. The first column of each csv is the number of added mass units from the monoisotopic mass of the peptide and the second column is the normalized intensity of each peak in the mass spectra.

Code/software

Chiclet Plot:
A chiclet plot is a grid-style chart (like a heatmap) where values are shown using rounded rectangles (“chiclets”) instead of plain squares. It’s mainly used to compare categorical data across two dimensions with color intensity.

Woods Plot (Forest Plot):
A woods/forest plot displays estimated results (like effect sizes) along with confidence intervals for multiple studies or groups. It’s commonly used in meta-analysis to visually compare variations and overall trends.

All data is in formats readable by python and excel. Code used to fit the bimodal spectra is available upon request to the corresponding author. 

Access information

Data was derived from the following sources:

• Collected by the authors of the paper.