{"id":2499,"date":"2022-12-16T20:48:38","date_gmt":"2022-12-17T02:48:38","guid":{"rendered":"https:\/\/kermitmurray.com\/msblog\/?page_id=2499"},"modified":"2022-12-25T11:28:00","modified_gmt":"2022-12-25T17:28:00","slug":"reddit-r-proteomics","status":"publish","type":"page","link":"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-proteomics\/","title":{"rendered":"Reddit r\/proteomics"},"content":{"rendered":"\n<div class=\"wp-block-caxton-grid relative\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-columns caxton-grid-block\" style=\"padding-top:0;padding-left:0;padding-bottom:0;padding-right:0;grid-template-columns:repeat(12, 1fr)\" data-tablet-css=\"padding-left:em;padding-right:em;\" data-mobile-css=\"padding-left:em;padding-right:em;\">\n<div class=\"wp-block-caxton-section relative\" style=\"grid-area:span 1\/span 8\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-section-block\" style=\"padding-top:5px;padding-left:5px;padding-bottom:5px;padding-right:5px\" data-mobile-css=\"padding-left:1em;padding-right:1em;\" data-tablet-css=\"padding-left:1em;padding-right:1em;\">\n<p><a href=\"https:\/\/www.reddit.com\/r\/proteomics\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>\/r\/proteomics\/<\/strong><\/a><\/p>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-caxton-section relative\" style=\"grid-area:span 1\/span 4\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-section-block\" style=\"padding-top:5px;padding-left:5px;padding-bottom:5px;padding-right:5px\" data-mobile-css=\"padding-left:1em;padding-right:1em;\" data-tablet-css=\"padding-left:1em;padding-right:1em;\">\n<p><strong><a href=\"https:\/\/www.reddit.com\/r\/proteomics.rss\" target=\"_blank\" rel=\"noreferrer noopener\">RSS<\/a><\/strong><\/p>\n<\/div><\/div>\n<\/div><\/div>\n\n\n<ul class=\"has-dates has-authors has-excerpts wp-block-rss\"><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1uujr59\/need_help_with_ssdna_aptamer_folding_and_docking\/'>Need help with ssDNA aptamer folding and docking workflow<\/a><\/div><time datetime=\"2026-07-12T16:14:25-05:00\" class=\"wp-block-rss__item-publish-date\">July 12, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/DoubtMysterious3059<\/span><div class=\"wp-block-rss__item-excerpt\">Hey everyone, I&#039;m working on a science fair project using ssDNA aptamers and I&#039;m stuck on the folding and docking workflow. The 3D nucleic acid folding web servers I tried keep crashing, so I&#039;m not sure how to get a clean 3D model from a raw sequence string. Once I get the 3D structures, my plan is to use something like HDOCK to run molecular docking against my target proteins to check the binding affinity scores. Does anyone have advice on a reliable workflow or better tools I should use for ssDNA folding and docking? Any extra help with the [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1uubowm\/saliva_proteomics_sample_preparation_issues\/'>Saliva Proteomics Sample Preparation Issues<\/a><\/div><time datetime=\"2026-07-12T10:24:29-05:00\" class=\"wp-block-rss__item-publish-date\">July 12, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Solid_Session_225<\/span><div class=\"wp-block-rss__item-excerpt\">Hi! Im struggling with my sample prep for saliva samples. I have established a high throughout SP3 digestion protocol using native saliva from cortisol Salivettes but is seems like I\u2019m carrying some contaminants through the whole process that end up in my 7500+ Sciex Qtrap instrument which gets heavily contaminated after about 1000 injections and even gives some Q0 discharge errors. I\u2019m running a targeted peptide method using a common C18 peptide column at a flow rate of 1ml\/min with standard solvents (0.1% Fa in H2O and 0.1% FA in ACN). the whole method is 4min but I\u2019m using a [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1utk51v\/need_help_with_ssdna_aptamer_folding_and_docking\/'>Need help with ssDNA aptamer folding and docking workflow<\/a><\/div><time datetime=\"2026-07-11T13:28:09-05:00\" class=\"wp-block-rss__item-publish-date\">July 11, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/DoubtMysterious3059<\/span><div class=\"wp-block-rss__item-excerpt\">Hey everyone, I&#039;m working on a science fair project using ssDNA aptamers and I&#039;m stuck on the folding and docking workflow. The 3D nucleic acid folding web servers I tried keep crashing, so I&#039;m not sure how to get a clean 3D model from a raw sequence string. Once I get the 3D structures, my plan is to use something like HDOCK to run molecular docking against my target proteins to check the binding affinity scores. Does anyone have advice on a reliable workflow or better tools I should use for ssDNA folding and docking? Any extra help with the [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1ustfpi\/what_does_your_post_processing_workflow_look_like\/'>What does your post processing workflow look like after DIA NN\/FragPipe with MBR?<\/a><\/div><time datetime=\"2026-07-10T16:59:41-05:00\" class=\"wp-block-rss__item-publish-date\">July 10, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/popcornnzerocoke<\/span><div class=\"wp-block-rss__item-excerpt\">I know the FragPipe\/DIA NN docs cover the basics but I would rather hear from people who actually run these pipelines daily When processing large DIA datasets with MBR, what happens after the software finishes? What does your verification workflow look like before you trust the results? How do you currently validate that the cross run transfers aren&#039;t inflating your FDR? Roughly how many hours per project does your team spend on this manual curation or refiltering? We&#039;re seeing conflicting reports on whether MBR is a reliable &quot;set and forget&quot; step or a major bottleneck requiring manual intervention. Curious how [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1uqkn5r\/i_am_searching_for_full_funded_metabolomics\/'>I am searching for full funded metabolomics workshop !<\/a><\/div><time datetime=\"2026-07-08T06:32:22-05:00\" class=\"wp-block-rss__item-publish-date\">July 8, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Middle-Box3509<\/span><div class=\"wp-block-rss__item-excerpt\">I am a PhD scholar in food tech department . I have been doing untargeted metabolomics for a time now for some biomarker detection. I want to learn some advanced techniques in metabolomics but i just couldnt find a proper workshop for that . submitted by \/u\/Middle-Box3509 [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1uo8p0w\/where_can_i_download_e_coli_dda_proteomics_raw\/'>Where can I download E. coli DDA proteomics raw files for PTM artifact control?<\/a><\/div><time datetime=\"2026-07-05T17:54:04-05:00\" class=\"wp-block-rss__item-publish-date\">July 5, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Firm-Oil6308<\/span><div class=\"wp-block-rss__item-excerpt\">Hi everyone, I performed DDA LC\u2013MS\/MS on mouse brain lysate (tryptic digest, non-enriched) and analyzed the data using PEAKS BSI for broad PTM searching. The software identified and mapped Ubiquitination (both lysine and non-lysine residue modifications). I reported them in my manuscript. During peer review, the reviewers raised a concern that some of the PTMs might be artifacts and suggested validating the findings using an E. coli lysate digest as a negative control. The issue is that I don\u2019t currently have access to E. coli samples or instrument time to generate new data. So I\u2019m looking for advice on: Where [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1umkj78\/why_arent_embedded_analytical_databases_more\/'>Why aren\u2019t embedded analytical databases more common in proteomics?<\/a><\/div><time datetime=\"2026-07-03T17:23:29-05:00\" class=\"wp-block-rss__item-publish-date\">July 3, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/SmoothPsychology3999<\/span><div class=\"wp-block-rss__item-excerpt\">Most proteomics workflows still rely on multiple disconnected tools (Python, R, search engines, etc.). Do you think embedded analytical databases could become a viable backend for proteomics analysis? I\u2019ve been exploring this idea in a recent preprint and would love feedback from the community! https:\/\/zenodo.org\/records\/21036067 submitted by \/u\/SmoothPsychology3999 [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1ukxw1i\/need_help_with_ptm_identification_using_iptopdown\/'>Need help with PTM identification using IP-Top-down MS<\/a><\/div><time datetime=\"2026-07-01T20:58:40-05:00\" class=\"wp-block-rss__item-publish-date\">July 1, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/InjuryJolly7432<\/span><div class=\"wp-block-rss__item-excerpt\">If anyone has done in-depth IP-Top down MS on proteins I could seriously use help! I\u2019ve isolated my POI and am trying to do to top-down MS on it but honestly I don\u2019t know what I\u2019m looking at\/looking for. I know I need to do a full scan first to identify my POI and the m\/z for it, but from there I\u2019m baffled on what to do. The examples my colleague left for me are only for proteins approx. 35 kDa and mine is around 62! Does anyone have any advice as to what to look at\/read to help me [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1ukgelp\/questionhow_to_predict_mutation_effect_with\/'>Question:How to predict mutation effect with protein model without traditional computation<\/a><\/div><time datetime=\"2026-07-01T09:04:02-05:00\" class=\"wp-block-rss__item-publish-date\">July 1, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Duanqi-<\/span><div class=\"wp-block-rss__item-excerpt\">submitted by \/u\/Duanqi- [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1uj7llq\/at_the_cutting_edge_of_using_proteomics_for\/'>\u201cAt the Cutting Edge of Using Proteomics for Cancer Treatment Guidance\u201d (Adam Dicker, MD, PhD, FA&#8230; | Cancer Patient Lab<\/a><\/div><time datetime=\"2026-06-29T22:50:51-05:00\" class=\"wp-block-rss__item-publish-date\">June 29, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Key-Principle6254<\/span><div class=\"wp-block-rss__item-excerpt\">submitted by \/u\/Key-Principle6254 [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1ui42cs\/reconstituting_a_protein_complex_from_commercial\/'>Reconstituting a protein complex from commercial recombinant proteins?<\/a><\/div><time datetime=\"2026-06-28T18:01:09-05:00\" class=\"wp-block-rss__item-publish-date\">June 28, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/hyperfinesplitting<\/span><div class=\"wp-block-rss__item-excerpt\">Hi everyone, my PI suggested, mainly to save time, that I could buy individually recombinant proteins and try to reconstitute a heterotrimeric protein complex in vitro for a DSF\/thermal shift assay, instead of co-expressing and co-purifying the complex. I\u2019m a bit skeptical because of potential issues with tags, buffers, stoichiometry, stability, and whether the complex would actually form and be homogeneous enough to give interpretable data. The goal would be to test small-molecule stabilizers. Has anyone successfully done this with commercial recombinant proteins? Did it work well enough for DSF, SEC, SPR, or similar assays? Any practical advice, experience, or [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/proteomics\/comments\/1uh4bac\/seeking_advice_learning_pathway_for_lcmsms\/'>Seeking advice: Learning pathway for LC-MS\/MS proteomics in neurodegeneration research?<\/a><\/div><time datetime=\"2026-06-27T14:34:11-05:00\" class=\"wp-block-rss__item-publish-date\">June 27, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Connect_Switch_1026<\/span><div class=\"wp-block-rss__item-excerpt\">Hi everyone, I am currently a basic education teacher and I\u2019ve recently started my Master&#039;s in Medical Sciences, focusing on neurodegeneration. I joined a newly formed research team, and while we are highly motivated, we currently lack expertise in proteomics\u2014which is exactly the area I want to specialize in to strengthen our lab. Our research investigates neurodegeneration in the elderly. Specifically, I will be working with CSF and plasma to identify neuroinflammatory biomarkers associated with blood-brain barrier (BBB) dysfunction. My project will heavily rely on liquid chromatography and mass spectrometry (LC-MS\/MS). Since I am starting from scratch in this specific [&hellip;]<\/div><\/li><\/ul>\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-wide\"\/>\n\n\n\n<h4 class=\"wp-block-heading\">Related Feeds<\/h4>\n\n\n<ul class=\"su-siblings\"><li class=\"page_item page-item-2733\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-analyticalchemistry\/\">Reddit r\/analyticalchemistry<\/a><\/li>\n<li class=\"page_item page-item-2707\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-genomics\/\">Reddit r\/genomics<\/a><\/li>\n<li class=\"page_item page-item-2473\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-massspectrometry\/\">Reddit r\/massspectrometry<\/a><\/li>\n<li class=\"page_item page-item-2705\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-metabolomics\/\">Reddit r\/metabolomics<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Related Feeds<\/p>\n","protected":false},"author":1,"featured_media":2498,"parent":2738,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2499","page","type-page","status-publish","has-post-thumbnail","hentry","entry"],"_links":{"self":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2499","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/comments?post=2499"}],"version-history":[{"count":4,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2499\/revisions"}],"predecessor-version":[{"id":2745,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2499\/revisions\/2745"}],"up":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2738"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/media\/2498"}],"wp:attachment":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/media?parent=2499"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}