CURTAIN—A unique web-based tool for exploration and sharing of MS-based proteomics data

<p><span style="background-color: rgb(246, 246, 246); color: rgb(38, 38, 38);">To&nbsp;facilitate&nbsp;analysis&nbsp;and&nbsp;sharing&nbsp;of&nbsp;mass&nbsp;spectrometry&nbsp;(MS)-based&nbsp;proteomics&nbsp;data,&nbsp;we&nbsp;created&nbsp;online&nbsp;tools&nbsp;called&nbsp;CURTAIN&nbsp;(</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);">)&nbsp;and&nbsp;CURTAIN-PTM&nbsp;(</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);">)&nbsp;with&nbsp;an&nbsp;accompanying&nbsp;series&nbsp;of&nbsp;video&nbsp;tutorials&nbsp;(</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);">).&nbsp;These&nbsp;are&nbsp;designed&nbsp;to&nbsp;enable&nbsp;non-MS&nbsp;experts&nbsp;to&nbsp;interactively&nbsp;peruse&nbsp;volcano&nbsp;plots&nbsp;and&nbsp;deconvolute&nbsp;primary&nbsp;experimental&nbsp;data&nbsp;so&nbsp;that&nbsp;replicates&nbsp;can&nbsp;be&nbsp;visualized&nbsp;in&nbsp;bar&nbsp;charts&nbsp;or&nbsp;violin&nbsp;plots&nbsp;and&nbsp;exported&nbsp;in&nbsp;publication-ready&nbsp;format.&nbsp;They&nbsp;also&nbsp;allow&nbsp;assessment&nbsp;of&nbsp;overall&nbsp;experimental&nbsp;quality&nbsp;by&nbsp;correlation&nbsp;matrix&nbsp;and&nbsp;profile&nbsp;plot&nbsp;analysis.&nbsp;After&nbsp;making&nbsp;a&nbsp;selection&nbsp;of&nbsp;protein&nbsp;&quot;hits&quot;,&nbsp;the&nbsp;user&nbsp;can&nbsp;analyze&nbsp;known&nbsp;domain&nbsp;structure,&nbsp;AlphaFold&nbsp;predicted&nbsp;structure,&nbsp;reported&nbsp;interactors,&nbsp;relative&nbsp;expression&nbsp;as&nbsp;well&nbsp;as&nbsp;disease&nbsp;links.&nbsp;CURTAIN-PTM&nbsp;permits&nbsp;analysis&nbsp;of&nbsp;all&nbsp;identified&nbsp;PTM&nbsp;sites&nbsp;on&nbsp;protein(s)&nbsp;of&nbsp;interest&nbsp;with&nbsp;selected&nbsp;databases.&nbsp;CURTAIN-PTM&nbsp;also&nbsp;links&nbsp;with&nbsp;the&nbsp;Kinase&nbsp;Library&nbsp;to&nbsp;predict&nbsp;upstream&nbsp;kinases&nbsp;that&nbsp;may&nbsp;phosphorylate&nbsp;sites&nbsp;of&nbsp;interest.&nbsp;We&nbsp;provide&nbsp;examples&nbsp;of&nbsp;the&nbsp;utility&nbsp;of&nbsp;CURTAIN&nbsp;and&nbsp;CURTAIN-PTM&nbsp;in&nbsp;analyzing&nbsp;how&nbsp;targeted&nbsp;degradation&nbsp;of&nbsp;the&nbsp;PPM1H&nbsp;Rab&nbsp;phosphatase&nbsp;that&nbsp;counteracts&nbsp;the&nbsp;Parkinson’s&nbsp;LRRK2&nbsp;kinase&nbsp;impacts&nbsp;cellular&nbsp;protein&nbsp;levels&nbsp;and&nbsp;phosphorylation&nbsp;sites.&nbsp;We&nbsp;also&nbsp;reanalyzed&nbsp;a&nbsp;ubiquitylation&nbsp;dataset,&nbsp;characterizing&nbsp;the&nbsp;PINK1-Parkin&nbsp;pathway&nbsp;activation&nbsp;in&nbsp;primary&nbsp;neurons,&nbsp;revealing&nbsp;data&nbsp;of&nbsp;interest&nbsp;not&nbsp;highlighted&nbsp;previously.&nbsp;CURTAIN&nbsp;and&nbsp;CURTAIN-PTM&nbsp;are&nbsp;free&nbsp;to&nbsp;use&nbsp;and&nbsp;open&nbsp;source,&nbsp;enabling&nbsp;researchers&nbsp;to&nbsp;share&nbsp;and&nbsp;maximize&nbsp;the&nbsp;impact&nbsp;of&nbsp;their&nbsp;proteomics&nbsp;data.&nbsp;We&nbsp;advocate&nbsp;that&nbsp;MS&nbsp;data&nbsp;published&nbsp;in&nbsp;volcano&nbsp;plot&nbsp;format&nbsp;be&nbsp;reported&nbsp;containing&nbsp;a&nbsp;shareable&nbsp;CURTAIN&nbsp;weblink,&nbsp;thereby&nbsp;allowing&nbsp;readers&nbsp;to&nbsp;better&nbsp;analyze&nbsp;and&nbsp;exploit&nbsp;the&nbsp;data.</span></p>