DOI: 10.71663/curtain.fc34-wd57
title: CURTAIN—A unique web-based tool for exploration and sharing of MS-based proteomics data

description: <p><span style="background-color: rgb(246, 246, 246); color: rgb(38, 38, 38);">To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data, we created online tools called CURTAIN (</span><a href="https://curtain.proteo.info/" rel="noopener noreferrer" target="_blank" style="background-color: rgb(246, 246, 246); color: rgb(31, 117, 185);">https://curtain.proteo.info</a><span style="background-color: rgb(246, 246, 246); color: rgb(38, 38, 38);">) and CURTAIN-PTM (</span><a href="https://curtainptm.proteo.info/" rel="noopener noreferrer" target="_blank" style="background-color: rgb(246, 246, 246); color: rgb(31, 117, 185);">https://curtainptm.proteo.info</a><span style="background-color: rgb(246, 246, 246); color: rgb(38, 38, 38);">) with an accompanying series of video tutorials (</span><a href="https://www.youtube.com/@CURTAIN-me6hl" rel="noopener noreferrer" target="_blank" style="background-color: rgb(246, 246, 246); color: rgb(31, 117, 185);">https://www.youtube.com/@CURTAIN-me6hl</a><span style="background-color: rgb(246, 246, 246); color: rgb(38, 38, 38);">). These are designed to enable non-MS experts to interactively peruse volcano plots and deconvolute primary experimental data so that replicates can be visualized in bar charts or violin plots and exported in publication-ready format. They also allow assessment of overall experimental quality by correlation matrix and profile plot analysis. After making a selection of protein &quot;hits&quot;, the user can analyze known domain structure, AlphaFold predicted structure, reported interactors, relative expression as well as disease links. CURTAIN-PTM permits analysis of all identified PTM sites on protein(s) of interest with selected databases. CURTAIN-PTM also links with the Kinase Library to predict upstream kinases that may phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson’s LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We also reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open source, enabling researchers to share and maximize the impact of their proteomics data. We advocate that MS data published in volcano plot format be reported containing a shareable CURTAIN weblink, thereby allowing readers to better analyze and exploit the data.</span></p>
description: <h4><strong style="background-color: rgb(255, 255, 255); color: rgb(11, 11, 11);">CURTAIN Frontend.</strong></h4><p><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">The workflow of CURTAIN is described in </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">. The input selection parameters for CURTAIN are selected through an inbuilt dropdown menu (step 4, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) and summarized in </span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="http://www.pnas.org/lookup/doi/10.1073/pnas.2312676121#supplementary-materials" rel="noopener noreferrer" target="_blank">Dataset S1</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">. Experimental metadata can be added in the same format as used by the PRIDE database (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r27" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">27</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (step 4, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). Retrieval of up-to-date Uniprot metadata (step 5, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) uses the Uniprot web API (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r22" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">22</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). Visualization of the quality controls: profile plot, global correlation matrix (step 6, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), volcano plot (step 7, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), bar graphs/violin plots (step 8, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), protein domain structure, and protein expression profile (step 9, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) employs Plotly (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://plot.ly/" rel="noopener noreferrer" target="_blank">https://plot.ly</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r45" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">45</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). In step 9, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">, domain structures, disease links, mutagenesis information, and pharmaceutical use are determined using Uniprot (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://www.uniprot.org/" rel="noopener noreferrer" target="_blank">https://www.uniprot.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r22" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">22</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), predicted structure using AlphaFold (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://alphafold.ebi.ac.uk/" rel="noopener noreferrer" target="_blank">https://alphafold.ebi.ac.uk/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r29" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">29</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r46" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">46</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), protein interactions deploying the STRING interaction database (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://string-db.org/" rel="noopener noreferrer" target="_blank">https://string-db.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r30" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">30</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) as well as the Interactome Atlas (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="http://www.interactome-atlas.org/" rel="noopener noreferrer" target="_blank">http://www.interactome-atlas.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r31" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">31</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) and tissue expression uses ProteomicsDB (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://www.proteomicsdb.org/" rel="noopener noreferrer" target="_blank">https://www.proteomicsdb.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r32" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">32</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">).</span></p><h4><strong style="background-color: rgb(255, 255, 255); color: rgb(11, 11, 11);">CURTAIN-PTM Frontend.</strong></h4><p><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">CURTAIN-PTM is designed using the same framework described above. The workflow of CURTAIN-PTM is described in </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">. Steps 1 to 8 in CURTAIN-PTM are the same as CURTAIN, except in step 3b, preprocessing of PTM data derived from MS-Fragger, Spectronaut, and DIA-NN requires implementation of scripts prior to proceeding with step 4 in </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">. The input selection parameters for CURTAIN-PTM are selected through an inbuilt dropdown menu (step 4, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) and summarized in </span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="http://www.pnas.org/lookup/doi/10.1073/pnas.2312676121#supplementary-materials" rel="noopener noreferrer" target="_blank">Dataset S1</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">. The visualization of experimentally determined PTM in each protein (step 10, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) and comparison of experimental and database PTMs (step 11 and step 13, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) are undertaken using Plotly (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://plot.ly/" rel="noopener noreferrer" target="_blank">https://plot.ly</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r45" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">45</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). For predictions of kinases that phosphorylate a phosphorylation site of interest (step 12, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), we deployed the web API from the Kinase Library (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://kinase-library.phosphosite.org/site" rel="noopener noreferrer" target="_blank">https://kinase-library.phosphosite.org/site</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r33" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">33</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). For selection of PTM databases (step 13, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), we used PhosphoSitePlus (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://www.phosphosite.org/" rel="noopener noreferrer" target="_blank">https://www.phosphosite.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r18" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">18</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), Protein Lysine Modification Database (PLMD) using downloaded data (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r19" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">19</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), CarbonylDB (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="http://carbonyldb.missouri.edu/CarbonylDB/index.php/" rel="noopener noreferrer" target="_blank">http://carbonyldb.missouri.edu/CarbonylDB/index.php/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r20" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">20</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), GlyConnect (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://glyconnect.expasy.org/" rel="noopener noreferrer" target="_blank">https://glyconnect.expasy.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r21" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">21</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), or Uniprot (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://www.uniprot.org/" rel="noopener noreferrer" target="_blank">https://www.uniprot.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r22" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">22</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). For PTM Motif analysis (step 9, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">), we used weblogo (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://logojs.wenglab.org/app/" rel="noopener noreferrer" target="_blank">https://logojs.wenglab.org/app/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r34" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">34</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). For multiple sequence alignments in CURTAIN-PTM, we used biomsalign (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://github.com/ppillot/biomsalign" rel="noopener noreferrer" target="_blank">https://github.com/ppillot/biomsalign</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">).</span></p><h4><strong style="background-color: rgb(255, 255, 255); color: rgb(11, 11, 11);">CURTAIN and CURTAIN-PTM Backend.</strong></h4><p><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">With CURTAIN and CURTAIN-PTM, the end user can save their working session (step 9 CURTAIN, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">, step 13 CURTAIN-PTM, </span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#fig01" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">Fig. 1</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) and receive a unique web link to retrieve and share the analysis containing both data and interactive plots. User sessional data are stored in JavaScript Object Notation (</span><a href="https://www.pnas.org/doi/full/10.1073/pnas.2312676121#core-r47" rel="noopener noreferrer" target="_blank" style="background-color: transparent; color: rgb(31, 117, 185);">47</a><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) format using a backend built with the Django web framework (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://djangoproject.com/" rel="noopener noreferrer" target="_blank">https://djangoproject.com</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) and Postgres database (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://www.postgresql.org/" rel="noopener noreferrer" target="_blank">https://www.postgresql.org</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">). The main purpose of this backend is to provide permanent user storage as well as permission management for data access. Through a system controlled by the backend, if a user chooses to log in using their ORCID (</span><u style="background-color: transparent; color: rgb(31, 117, 185);"><a href="https://orcid.org/" rel="noopener noreferrer" target="_blank">https://orcid.org/</a></u><span style="background-color: rgb(255, 255, 255); color: rgb(38, 38, 38);">) credential, the saved session can be bound to their account and they can control whether other users can access the session data.</span></p><p></p>