DOI: 10.5281/zenodo.5205565
title: Protein Identification by Nanopore Peptide Profiling

description: This dataset belongs to “Protein Identification by Nanopore Peptide Profiling” and describes the raw data and analysis of tryptic digested peptides translocating through a mutant Fragaceatoxin C nanopore. A jupyter notebook describing the analysis and structure is added to this dataset. <strong>Data description:</strong> <strong>Protein Identification by Nanopore Peptide Profiling.ipynb</strong> Jupyter notebook contained data analysis of data contained in data_0.zip and data_1.zip (Python 3.7) <strong>python_scripts.zip</strong> Supplementary scripts belonging to “Protein Identification by Nanopore Peptide Profiling.ipynb”. See explanation of custom classes in the jupyter notebook. <strong>data_0.zip</strong> - Folder containing raw electrophysiology data and result after analysis with “Protein Identification by Nanopore Peptide Profiling.ipynb”, with each folder containing the following: Alpha casein: Tryptic digest of alpha casein Beta casein: Tryptic digest of beta casein BSA: Tryptic digest of bovine serum albumin Control: Tryptic digest of water (no protein, control measurement) Cytochrome c: Tryptic digest of cytochrome c DHFR_His6: Tryptic digest of dihydropholate reductase (His6 tagged) EFP: Tryptic digest of elongation factor P HMW1Act: Tryptic digest of high molecular weight adhesin protein <strong>data_1.zip</strong> - Folder containing raw electrophysiology data, comma-separated MS peptide masses, and result after analysis with “Protein Identification by Nanopore Peptide Profiling.ipynb”, with each folder containing the following: Lysozyme: Tryptic digest of lysozyme PAN: Tryptic digest of proteasome-activating nucleotidase TbpA_Y27A: Tryptic digest of periplasmic binding protein Trypsin: Tryptic digest of bovine trypsin Mass_spec: csv files containing measured ESI-MS peptides Lysozyme synthetic peptides: Synthetic peptides: Lys1: TPGSR Lys2alk: C(+57.02)ELAAAMK Lys3: HGLDNYR Lys4alk: WWC(+57.02)NDGR Lys5: GTDVQAWIR Lys6alk: GYSLGNWVC(+57.02)AAK Lys7: FESNFNTQATNR The structure of the data files is registered data_1.zip in <strong>'index.csv'</strong> (digested proteins) and <strong>'index</strong><strong>_peptides</strong><strong>.csv'</strong> (synthetic peptides) contained in the data folder. In this file, we describe the protein that was measured as well as the folder location and the expected baseline / standard deviation.<br> <br> <strong>Structure of <em>./data/index.csv</em></strong> <strong>Protein (string) | Folder (string) | Baseline (pA) (float) | Baseline Error (pA) (float)</strong> In each <strong>Folder</strong>, there is another <strong>'index.csv'</strong>, explaining which files are with protein and which are without (blank).<br> <br> <strong>Structure of <em>./data/[protein]/[repeat]/index.csv</em></strong> <strong>blank (boolean) | fname (string)</strong> Each folder in data_0.zip and data_1.zip contains a folder for each measure protein, which contains a folder for each repeat. The repeats contain raw axon binary files (.abf), each file contains measurement conditions as follows: [Date of measurement]_[Pore type]_[Buffer conditions]_[added analyte(s)]_[operator initials] <em>e.g</em>: 20200312_1M_KCl_50mM_Citricacid_50mM_BTP_pH_38_FraC_G13F_neg70mV_20ul_CytC_TrypsinGold_FL_0000 Measured on 12-03-2020, in 1M KCl buffered with Citricacid (50 mM) adjusted using bis-tris-propane to pH 3.8, using Fragaceatoxin C mutant G13F at a negatively applied potential of 70 mV. 20 µL cytochrome c was added to the cis compartment. The total volume of the container used for all electrophysiology experiments was 400 µL, all samples were prepared at a 1 g/L concentration. A prefix “perf” before analyte description indicates that the chamber was flushed with approximately 2 mL fresh buffer prior to analysis. The buffer condition "BTP" means bis-tris-propane, which is used to titrate to the exact pH of 3.8. Each analysed folder contains<strong> results.pkl</strong> file, containing the analysis result as provided by “Protein Identification by Nanopore Peptide Profiling.ipynb” - see the jupyter notebook Each analysed folder contains <strong>results_analysis.xlsx</strong>, which contains sheets with excluded currents, standard deviations, dwell time and beta value for the pore without analyte added “Blank” and results from the analyte added in “Results”. Parameters used for fitting are contained in “Parameters”. The “Histograms” tab shows the raw data of the excluded current spectra. <strong>mass_spec_peaks.zip</strong> – Folder containing mass spectrometry files as analysed by PEAKS Studio The folder contains an subfolder for each protein measured using electrospray ionisation mass spectrometry (ESI-MS). acasein: alpha casein protein b_casein: beta casein protein BSA: bovine serum albumin CytC: cytochrome C digested DHFR: dihydropholate reductase HMW1_Act: high molecular weight adhesin protein PAN: proteasome-activating nucleotidase ThBP: periplasmic thiamine binding protein Trypsin: bovine trypsin
description: This work is part of the research program of the Foundation for Fundamental Research on Matter (FOM), which is part of the Netherlands Organization for Scientific Research (NWO) under grant number 16SMPS05. In addition, M.T.C.W. was supported by the Dutch Organization for Scientific Research (VENI 722.016.006).