tag:blogger.com,1999:blog-36932380145256505732024-03-18T00:44:48.127-07:00News in Proteomics Researchnow also at www.proteomics.rocksUnknownnoreply@blogger.comBlogger2881125tag:blogger.com,1999:blog-3693238014525650573.post-47145315704801474552024-03-15T12:40:00.000-07:002024-03-16T06:19:47.108-07:00THUNDER-PASEF - Get those real immunopeptides! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhtzCJ-7joi2rU6eTyP-O27Rb8ylxG3NMl-_y1QPLDZZ0SDXLRTJC0M6IWn-6BGaBjWK6gFQj8EkGV9w06BLYnIJGGNacj5Au2rhwrV0HudFQw1QmEVdaYI_z7_00ORQuwtOJKNIN-XGAp7_CmxFxFm5JKMbJoNGzf4iAJ14v7YlLWTdFZx2z0Urj-5fU0" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="465" data-original-width="730" height="339" src="https://blogger.googleusercontent.com/img/a/AVvXsEhtzCJ-7joi2rU6eTyP-O27Rb8ylxG3NMl-_y1QPLDZZ0SDXLRTJC0M6IWn-6BGaBjWK6gFQj8EkGV9w06BLYnIJGGNacj5Au2rhwrV0HudFQw1QmEVdaYI_z7_00ORQuwtOJKNIN-XGAp7_CmxFxFm5JKMbJoNGzf4iAJ14v7YlLWTdFZx2z0Urj-5fU0=w532-h339" width="532" /></a></div><br /><p></p><p><a href="https://www.nature.com/articles/s41467-024-46380-y?utm_source=dlvr.it&utm_medium=twitter">I need more time to spend on this, but I'm going to put it here anyway</a>. </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEidYjLXoo7es0lLa1GSgbLdotxV_NaSVK4I2m_E-K4SOVCCRljmCY_34PmViMuVQdnuQ9Wkp_XWFPa4ZU6cQyoYaqhFwCTeu9Gs0MW-7cOU3zk5q90J82Q6AkrNyGQU4Du0X7XVFrN2so6QfMGoNKTtSOPrCd8G4kOlLpGUh0Gc4gVwjxCWLdAmObMxNPM" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="517" data-original-width="798" height="346" src="https://blogger.googleusercontent.com/img/a/AVvXsEidYjLXoo7es0lLa1GSgbLdotxV_NaSVK4I2m_E-K4SOVCCRljmCY_34PmViMuVQdnuQ9Wkp_XWFPa4ZU6cQyoYaqhFwCTeu9Gs0MW-7cOU3zk5q90J82Q6AkrNyGQU4Du0X7XVFrN2so6QfMGoNKTtSOPrCd8G4kOlLpGUh0Gc4gVwjxCWLdAmObMxNPM=w534-h346" width="534" /></a></div><br /><p></p><p>What's this about? </p><p>Based on comments I've received about what I write recently I'm going to be trying to provide what I think is important context in anything I review. Obviously, context is from my perspective and background</p><p>Okay, so HLA peptides are super annoying to analyze but they are very very important. These little peptides are on the surface of our cells and they are part of the system that tells our immune system DON'T EAT ME. It's all self-self recognition stuff, sort of. When that system isn't working perfectly it's bad. Cells that are diseased (like cancer cells) aren't being targeted and destroyed. When it is working too well, it is also bad (auto-immune problems). So it's important that we can categorize those cells on the surface. HLA Class II are easier. The peptides are bigger and easier to sequence. Not easy, per se, but easier than Class I.</p><p>Class I peptides are much smaller than the ideal targets for mass spectrometry. Also, as they are produced after proteosomal degradation, it is very unlikely that the amino acid on the end is a lysine or arginine. Which is the opposite of useful for mass spec based sequencing.</p><p><a href="https://proteomicsnews.blogspot.com/2019/02/doing-mhchla-peptidomics-please-stop-if.html">And - we've known for a long time that just running a standard proteomics method on HLA peptides is suboptimal. </a> Now that I'm an academic, I am wondering why I didn't publish that..... I probably should....</p><p>So...how would you go about doing this if you had a really nice 200 resolution ion mobility instrument on the front of a mediocre mass spectrometer? </p><p>THUNDER! <a href="https://www.youtube.com/watch?v=v2AC41dglnM">Na na na na na-na-na-na</a> (caution: actually the video link. might be loud)</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEg3YvIms9QbwLTdFaBNxXbBX6JE-kit4lENYURNb0CDg3C7yw78AN0_ORlOIBlW1srYpOn14RbAYQ-CnIB_t6ZPYJ2NdWE8YC3fEc_lD2PxOvTAGTPP9bgsik24nOs5tuR_oeAUxPEtHEgX_SDQ-KsO6ptUCSMgyxm688FdZWiQvq-Hx98ooDg9MyaHjHQ" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="573" data-original-width="732" height="364" src="https://blogger.googleusercontent.com/img/a/AVvXsEg3YvIms9QbwLTdFaBNxXbBX6JE-kit4lENYURNb0CDg3C7yw78AN0_ORlOIBlW1srYpOn14RbAYQ-CnIB_t6ZPYJ2NdWE8YC3fEc_lD2PxOvTAGTPP9bgsik24nOs5tuR_oeAUxPEtHEgX_SDQ-KsO6ptUCSMgyxm688FdZWiQvq-Hx98ooDg9MyaHjHQ=w466-h364" width="466" /></a></div><br />Okay, so from Figure 2 it doesn't look like Thunder makes a lot of sense, it looks more like you should just not use a TIMS octagon. Which.....in my experience has never ever been a good thing...<p></p><p>Get further into the paper when they model the octagons. It definitely improves things. <br /></p><p>Big takeaway here could be - YOU CAN USE MORE THAN 1 TIMS OCTAGON! I did know this, but I didn't learn it until a few months ago. <a href="https://stockanalysis.com/stocks/brkr/revenue/">The company that had a 2023 revenue of almost $3 BILLION</a> still hasn't found the money to make any instruction manuals for said instruments, but that's understandable, of course.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRZ3We7R9FQmmJ-YiugfFrkst0Ohw-ydx3H_PC-rUZyiAJaSnZZ-OuW9oz29RmlPCzTIRb9BcdazBx-vVvId70Zciy7QsjA8NQfALhPIRfJ6Ztd90HWn6HFPyudkA8V_Ti1EIYVSzDTEgsmS_ATvhu7H11183oXO1slU1LU9QwXNIcWtwDx-ChGE7NC-E/s220/scrooge-mcduck.gif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="169" data-original-width="220" height="350" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRZ3We7R9FQmmJ-YiugfFrkst0Ohw-ydx3H_PC-rUZyiAJaSnZZ-OuW9oz29RmlPCzTIRb9BcdazBx-vVvId70Zciy7QsjA8NQfALhPIRfJ6Ztd90HWn6HFPyudkA8V_Ti1EIYVSzDTEgsmS_ATvhu7H11183oXO1slU1LU9QwXNIcWtwDx-ChGE7NC-E/w456-h350/scrooge-mcduck.gif" width="456" /></a></div><p>But the numbers here are solid. The gold standard for immunopeptidomics is around 50 milligrams because that's about the size of a normal biopsy punch sample. If you assume 30% of that is protein you're at 16mg or something. If you start with 100 million human cells, assuming a protein content of around 200 picograms/cell you're at 20-ish mg of material! </p><p>If you work out HLA peptides from 100 million cells, you're at a level where you might actually help find a cell surface marker that could be used to inform an immunotherapeutic therapy - or - design a new personalized therapeutic to target and destroy that tumor. And this is where we've been trying to get to from a sensitivity perspective for a long time. </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-66864017172693436842024-03-14T09:15:00.000-07:002024-03-15T09:52:15.853-07:00I missed the 20th US Human Proteomics Organization meeting! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhmoeNr8jqM67jxUZzVQonC_gfoJ6-N9OWUvoSI7DS2u0Heo4l1I9Fw9dmFFx3RiiUXLOw_L4uMW3jrKRaMAoBII_jGfHUK1RI2NIHGfbhXsuFHLNGNd_-79Uep7SPzvAEk5INvYmUFEm2jWIttTrBRqDucus2hPtXtxO8f0ftR18sQpxHvV8dTGpAFx4A" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="820" data-original-width="1920" height="228" src="https://blogger.googleusercontent.com/img/a/AVvXsEhmoeNr8jqM67jxUZzVQonC_gfoJ6-N9OWUvoSI7DS2u0Heo4l1I9Fw9dmFFx3RiiUXLOw_L4uMW3jrKRaMAoBII_jGfHUK1RI2NIHGfbhXsuFHLNGNd_-79Uep7SPzvAEk5INvYmUFEm2jWIttTrBRqDucus2hPtXtxO8f0ftR18sQpxHvV8dTGpAFx4A=w532-h228" width="532" /></a></div><br /><p></p><p>I missed the 20TH MEETING OF THE US HUMAN PROTEOMICS ORGANIZATION thanks to my immune system being a slacker. The committee I chair, the <a href="https://www.ushupo.org/Committees">US HUPO Virtual Media Outreach Committee</a> (most of the group is above) sent me pictures like this. </p><p>I just found this and I'm brazenly stealing it -- </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgGdjfzYK3OjRjzyfiTNVRUatdq1k-o-V98KbnyfZluZo6lvOwbsoxyjJ_d0v8sgfUjr5TXsX7eSFz2fx9hm79Jc9Xm9Qjd5bG1iqiontWU-ry-n2EcDo7odWqj6pFJ8Gs4m1aTg2tgOAUEBkOq4OKXgNlhh1dwFqxeUJJyLqEQB_FxIfWo2iRsfbQg7UQ" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1124" data-original-width="926" height="501" src="https://blogger.googleusercontent.com/img/a/AVvXsEgGdjfzYK3OjRjzyfiTNVRUatdq1k-o-V98KbnyfZluZo6lvOwbsoxyjJ_d0v8sgfUjr5TXsX7eSFz2fx9hm79Jc9Xm9Qjd5bG1iqiontWU-ry-n2EcDo7odWqj6pFJ8Gs4m1aTg2tgOAUEBkOq4OKXgNlhh1dwFqxeUJJyLqEQB_FxIfWo2iRsfbQg7UQ=w413-h501" width="413" /></a></div><br />Is this the same meeting that we'd been trying to interview all the invited speakers for? Yes. Well...not all of them, THE Proteomics Show has to fit into space around our jobs and families and things, but we got a bunch of them. <p></p><p>The same meeting that the spent months working on so we could have a cool proteomics video competition? Yes. Same one. Super bummed to miss it. </p><p>The winning video was a parody video called "The Real Scientists of Beverly Hills" and came from Cedar Sinai. The concept makes me laugh every time I think about it, even though I didn't see it. </p><p>Because proteomics is now (FINALLY) a thing the outside world thinks about once in a while - legit news outlets sent legit reporters. <a href="https://www.genengnews.com/topics/omics/proteomics-in-portland-a-video-update-from-the-us-hupo-conference/">Not joking. Here is a link!</a> </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEi-UbfS9B_lm0_4l8u70xXtkPab6fx37WF6l_pJtulpm8YpRXMYyswcxRwSmsWmZuzUPm3mqAYecwZC9tZa5jrmF2FEM5tWvaVqHP3r-cOpcmVpUXao6IUSL5W4gdp-A0vv7aev-cN64_pZqsxGgvYM_vHmYxCJNe26eUX_eqnGplK7Us9hjwKaSqnN1rQ" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="875" data-original-width="959" height="420" src="https://blogger.googleusercontent.com/img/a/AVvXsEi-UbfS9B_lm0_4l8u70xXtkPab6fx37WF6l_pJtulpm8YpRXMYyswcxRwSmsWmZuzUPm3mqAYecwZC9tZa5jrmF2FEM5tWvaVqHP3r-cOpcmVpUXao6IUSL5W4gdp-A0vv7aev-cN64_pZqsxGgvYM_vHmYxCJNe26eUX_eqnGplK7Us9hjwKaSqnN1rQ=w460-h420" width="460" /></a></div><p><br /></p>The 60 second lightening talks at US HUPO are, of course, legendary. Apparently there was some beatboxing. If you've never seen these rapid fire talks, you're missing out. Again - sooooo bummed I wasn't there. <p></p><p>THE Proteomics Show still happened, just with a <a href="https://lab.vanderbilt.edu/rasr-lab/our-group/our-team/">legitimate upgrade of one of the hosts!</a> (Whoa. RASR lab website is seriously cool....) </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjGW87Qy7RE8W-UlePGlfQxjaA82VmjumdCKI0s4vMDYc5Z0qsRKDSaJqxVp80kXjgYhjph-_CWgadV9hn46KAMj5S_uyuZac3iIcPD3u9IPrIS0KglPblAv5W8-ykIifVolPlST73EqE-thitkb7_wxY2Igac9KI-tNzqGmJofvJvH8a0l7zNc8_NvqCM" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="363" data-original-width="527" height="335" src="https://blogger.googleusercontent.com/img/a/AVvXsEjGW87Qy7RE8W-UlePGlfQxjaA82VmjumdCKI0s4vMDYc5Z0qsRKDSaJqxVp80kXjgYhjph-_CWgadV9hn46KAMj5S_uyuZac3iIcPD3u9IPrIS0KglPblAv5W8-ykIifVolPlST73EqE-thitkb7_wxY2Igac9KI-tNzqGmJofvJvH8a0l7zNc8_NvqCM=w487-h335" width="487" /></a></div><br />I have every intention of listening to this one (it will be the first one) when it goes live. Maybe today? <p></p><p>Big shoutout to the award winners this year. I am ultra bummed to have missed </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhvkavQMApoa2iO8gqxrkTvGH0EbaQDnw44B8hApAT8CzHm5j43pntnUAF4a_3lIMkjfMaTvJk38-4MNqdfi8wAk3wngxIqbm8--xbFmhrrn1lyStQIPfavG7GJ32f0qAEe5JUvosCi-4A0yvnpLIlPQLT0nzQ6_QLSLYPQ7CBT9dCAa_K6QNT62P5nE0Y" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1667" data-original-width="2500" height="213" src="https://blogger.googleusercontent.com/img/a/AVvXsEhvkavQMApoa2iO8gqxrkTvGH0EbaQDnw44B8hApAT8CzHm5j43pntnUAF4a_3lIMkjfMaTvJk38-4MNqdfi8wAk3wngxIqbm8--xbFmhrrn1lyStQIPfavG7GJ32f0qAEe5JUvosCi-4A0yvnpLIlPQLT0nzQ6_QLSLYPQ7CBT9dCAa_K6QNT62P5nE0Y" width="320" /></a></div><br />Kelleher's Don Hunt award! <p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEj7GWbP_yUwsMcevjmGX27h2xwrNmSndi3hh5VBzfWktqfTt6kaZyOcqnWg5uTSmZ7BpUGtn9tTAKky-xcGeOA-zP6x7xmAsV6kZgJcKZLY_IlPJGU5axlIyTchLtbeSNO0214jwlu546hhuxKzPA9mIoquMlKy5EVd3MMGrJjlgsk6xxd2Iyh4ZRR9Qbg" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="864" data-original-width="1023" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEj7GWbP_yUwsMcevjmGX27h2xwrNmSndi3hh5VBzfWktqfTt6kaZyOcqnWg5uTSmZ7BpUGtn9tTAKky-xcGeOA-zP6x7xmAsV6kZgJcKZLY_IlPJGU5axlIyTchLtbeSNO0214jwlu546hhuxKzPA9mIoquMlKy5EVd3MMGrJjlgsk6xxd2Iyh4ZRR9Qbg" width="284" /></a></div><br />Parag's Computational Award winning talk! <p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiLb-Yi1YNDm5NhXu1UCIJ-N5E-OeJyWkJFwDD9Vlf1VVRN-43ovQzDrdDiJEi7T_yo-C_314PSNFaYspiUGaaV83hPw5VOZjTuanLh2ybLYKHeYdU9CLCJqXLuWhL1Ijr6f61oXRCIJ61nhEaB65gicTaqVqvZX0ym5vOHSDhk0G9PFitg_sf1G9ePIxE" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="276" data-original-width="497" height="178" src="https://blogger.googleusercontent.com/img/a/AVvXsEiLb-Yi1YNDm5NhXu1UCIJ-N5E-OeJyWkJFwDD9Vlf1VVRN-43ovQzDrdDiJEi7T_yo-C_314PSNFaYspiUGaaV83hPw5VOZjTuanLh2ybLYKHeYdU9CLCJqXLuWhL1Ijr6f61oXRCIJ61nhEaB65gicTaqVqvZX0ym5vOHSDhk0G9PFitg_sf1G9ePIxE" width="320" /></a></div><br />Jenny van Eyk's always inspirational talks on why we NEED PROTEOMICS IN THE CLINIC. YESTERDAY. <p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjNqtHXuQxxJxLiNijRies8yF6rtjuuLGuGWS4SQd2xQvS9ytff14tSMd2fY96k7q53Tqu7s-XA18YXnwl7EKUq0N0ZyTWc6fTTN3LFIC16rrv9bn46RB7p4aJWdB3UXf6EYa54LovuvYG0XzoL7rD5PxhYC1BNC8aKG6a20Ye_dZ1j6I5hl6Euv5ZcK3c" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="719" data-original-width="810" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEjNqtHXuQxxJxLiNijRies8yF6rtjuuLGuGWS4SQd2xQvS9ytff14tSMd2fY96k7q53Tqu7s-XA18YXnwl7EKUq0N0ZyTWc6fTTN3LFIC16rrv9bn46RB7p4aJWdB3UXf6EYa54LovuvYG0XzoL7rD5PxhYC1BNC8aKG6a20Ye_dZ1j6I5hl6Euv5ZcK3c" width="270" /></a></div><p><br /></p>And the Cotter Early Investigator Award winning talk by Ying Zhu<p></p><p>I like good award winning talks as much as anyone, but posters are my favorite part of any conference. That's where you get to meet the smart young people who are actually in the trenches running the instruments and pushing the limits of what we can do with any proteomics technology. CRITICALLY ULTRA BUMMED. Next time.</p><p>If you haven't heard - US HUPO 2025 is PHILADELPHIA!!</p><p>Also - have you ever been to a conference that was really disorganized? Like you can't figure out where things are going on at each point in time or stuff starts too early or too late? You know why this doesn't happen at this one? US HUPO has </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgR5-nBrvGYmqkCP-dWMtVG1CWZEI3DGgjNujlaa6PMzR2Ew4zqSwbWcexuyJAy8I5PQPml2Ii1iiIH5KrlIe9q0UOIQgE62sBdlZ_ynmrn9Wtmdx9Bjx3XPW5ZXFmltaAfdDNi23QDyHnTFC8c_wW3mYuZEYikwAGWt-EJxnJWbQcwj-Ynr36X9s2r4A/s1581/ConferenceSolutions.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="780" data-original-width="1581" height="258" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgR5-nBrvGYmqkCP-dWMtVG1CWZEI3DGgjNujlaa6PMzR2Ew4zqSwbWcexuyJAy8I5PQPml2Ii1iiIH5KrlIe9q0UOIQgE62sBdlZ_ynmrn9Wtmdx9Bjx3XPW5ZXFmltaAfdDNi23QDyHnTFC8c_wW3mYuZEYikwAGWt-EJxnJWbQcwj-Ynr36X9s2r4A/w524-h258/ConferenceSolutions.JPG" width="524" /></a></div><br /><p>From left to right (ignore Pratik, Lydia, Jennifer and Brianna, ignore Ben) from <a href="https://www.conferencesolutionsinc.com/">Conference Solutions</a>. And they make all the things work! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-64708517379619081882024-03-13T07:57:00.000-07:002024-03-13T08:06:03.810-07:00Separate single cells, extract metabolites and ionize them in one go! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjQwTJh3nYYJVh6Zz1d6AykW0ksdr_DnhV1BkuYfyY-GqZC4mb2p4yno9XgGSg4aaJWD4cJWeIYCwKlC4qwHDKlQwLMhSQXvk_mZlnSkJ949GNw5Cyzhn2WZJWFCJjfRm68KpHFYMkeFoD6Elv-8Y8aFSHl57Qo21eo5FdMJ9BIHIVb-Rn_EBPGtGDwfCA" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="759" data-original-width="581" height="473" src="https://blogger.googleusercontent.com/img/a/AVvXsEjQwTJh3nYYJVh6Zz1d6AykW0ksdr_DnhV1BkuYfyY-GqZC4mb2p4yno9XgGSg4aaJWD4cJWeIYCwKlC4qwHDKlQwLMhSQXvk_mZlnSkJ949GNw5Cyzhn2WZJWFCJjfRm68KpHFYMkeFoD6Elv-8Y8aFSHl57Qo21eo5FdMJ9BIHIVb-Rn_EBPGtGDwfCA=w363-h473" width="363" /></a></div><p></p><p>I'm going to bore (boor? bour?) anyone unlucky enough to visit this awful blog because <a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c05741">this study is on:</a></p><p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c05741">Single cells</a></p><p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c05741">AND </a></p><p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c05741">Metabolomics</a></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiR3Djw6YLZ1M6oOTgd3K7GvrrT85uOj8paETFTBG64fZxdQLzSE7WlvM33r16mhmR7sF2HyeP49V02fCkPm6OLvhJWu77YoxW-gNZokkmIhULgVpWnQjSegXPtfmZ3W1XvnofIUnS4ZPGarkl-4NK3cs1Y0eR9p7GTahsBSGCKPJvo4cxAhyslO6IzI_k" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="322" data-original-width="863" height="187" src="https://blogger.googleusercontent.com/img/a/AVvXsEiR3Djw6YLZ1M6oOTgd3K7GvrrT85uOj8paETFTBG64fZxdQLzSE7WlvM33r16mhmR7sF2HyeP49V02fCkPm6OLvhJWu77YoxW-gNZokkmIhULgVpWnQjSegXPtfmZ3W1XvnofIUnS4ZPGarkl-4NK3cs1Y0eR9p7GTahsBSGCKPJvo4cxAhyslO6IzI_k=w504-h187" width="504" /></a></div><p>This is a 3D printed ionization source that allows you to put in a population of cells. Then the cells have to go in single file because they are being pushed down something too small for them to bunch up in.</p><p>While they are being pushed through the metabolites are extracted out of them!</p><p>THEN the metabolites are directly ionized into an Orbitrap (looks like a Classic!)</p><p>And...no joke, it actually looks like it works.</p><p>If you're following along in the statistics world, someone recently realized that there are problems with some of the advanced statistics used in single cells. We'll ignore it right now 'cause the dust may settle one day, but according to these plots, they can tell different cancer cells apart using this crazy source!</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhpdKWyPqP7ucHsQ9NlUmkqmgkPqs01xgFxIyMiXfInGcSW0CrKpkQcND51yTydgV6Vv8E4ixroBtKlkvV71Kudh_26JaCjuiCzMG2XtyVXX-TU7mFEZkAHk1Z7gpSXmzg26s9S3DvqC-DwNtBhSftD-CPYkUc-bQaMd3ZINfjP0CGnOAVh0UNXMcoMR4c" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="234" data-original-width="434" height="228" src="https://blogger.googleusercontent.com/img/a/AVvXsEhpdKWyPqP7ucHsQ9NlUmkqmgkPqs01xgFxIyMiXfInGcSW0CrKpkQcND51yTydgV6Vv8E4ixroBtKlkvV71Kudh_26JaCjuiCzMG2XtyVXX-TU7mFEZkAHk1Z7gpSXmzg26s9S3DvqC-DwNtBhSftD-CPYkUc-bQaMd3ZINfjP0CGnOAVh0UNXMcoMR4c=w422-h228" width="422" /></a></div><br /><p></p><p></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-40788605775832890232024-03-12T04:47:00.000-07:002024-03-13T05:02:34.614-07:00FUNCTIONAL spatial proteomics is live! <p></p><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrIa2tVBqzcwm0YC0LEueHUyHzeTGCiRp4Ts3KhspCzDObaTQshSxgTylr2uMXYLkeQ5vx_ecyueNEInkuzOtjGohX3K26VwAXVeXkMOooSyO_aSPaoeKt2CI2kXYauxdhkH0J5RWaM4_CxC4H5NTO7x7TztfHDziF-94dOAXqZju7KqiZ6LDyxerc4us/s1297/Mapping_microhabitats_with_functional_spatial_proteomics.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="924" data-original-width="1297" height="355" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrIa2tVBqzcwm0YC0LEueHUyHzeTGCiRp4Ts3KhspCzDObaTQshSxgTylr2uMXYLkeQ5vx_ecyueNEInkuzOtjGohX3K26VwAXVeXkMOooSyO_aSPaoeKt2CI2kXYauxdhkH0J5RWaM4_CxC4H5NTO7x7TztfHDziF-94dOAXqZju7KqiZ6LDyxerc4us/w498-h355/Mapping_microhabitats_with_functional_spatial_proteomics.JPG" width="498" /></a></div><br /><p></p><p><a href="https://www.nature.com/articles/s41589-023-01536-7">In a very early entry for paper of the year....</a></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjnIaHa4w2yEJ7CgnSMfn3Hwh3n1gXaLxDJMXQx2UgVLyY5jwIvdW6VHnNngwtfdaHyWx25aOfkLY_FLOgoY3wQxUGdCVrZVOxEHBk-_gy0ZBiOVD3Lldqq1nlgDl3XEnGx3bbj-cjM3cHoROwO-hJr1gbYj0DxLoINFpoSTor-spanu9aA2U9WrM73p4U/s777/MappingMicrohabitatsSpatialProteomicsPaper.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="556" data-original-width="777" height="321" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjnIaHa4w2yEJ7CgnSMfn3Hwh3n1gXaLxDJMXQx2UgVLyY5jwIvdW6VHnNngwtfdaHyWx25aOfkLY_FLOgoY3wQxUGdCVrZVOxEHBk-_gy0ZBiOVD3Lldqq1nlgDl3XEnGx3bbj-cjM3cHoROwO-hJr1gbYj0DxLoINFpoSTor-spanu9aA2U9WrM73p4U/w449-h321/MappingMicrohabitatsSpatialProteomicsPaper.JPG" width="449" /></a></div><br /><p>Quick overview - one of the goals of any sort of bioenergy production has been to figure out how the actual fuck microorganisms break down cellulose into usable energy sources without literally catching it on fire. If you can release the base sugar molecules trapped in WOOD you could do easy things like convert that to ethanol or butanol or other handy things. </p><p>The problem is that these things are not happening in a homogeneous way. There are typically diverse populations of organisms widely dispersed throughout the material that are doing these things. </p><p>How do you decide where to actually focus your efforts? </p><p>How do you know that where you are analyzing is actually where the cool stuff is happening? </p><p>Do what this groundbreaking work at PNNL is doing! You first slice your material and you use mass spectrometry imaging (they're using MALDI-FITCR I think) to locate the breakdown molecules that you are interested in.</p><p>THEN you take that same material off and you cut tiny tiny tiny tiny sections out of the area where those molecules came from. They're using NanoPots / MicroPots and then doing proteomics / metaproteomics. </p><p>So now they know what enzymes are directly linked to the small spatial area where the lignocellulose breakdown products are coming from! Killer, right? Okay, but get this, why can't you just use this exact same system and apply it to other biological materials? We got a glimpse of what is coming down the pipeline from PNNL when we interviewed Dr. Burnum-Johnson on THE Proteomics Show earlier this year. There is something coming that is definitely worth setting a google scholar alert on this PI's name. </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-1604011501276192182024-03-11T09:41:00.000-07:002024-03-13T05:02:55.589-07:00Single particle analysis enabled by 25 second transient times! <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhyxYpzmWN-tpl0LxNLefuCTyDQBWJB-6zhHZxqf7odLrwSn7AfjqgYoeT_AThr0sdtuefWFqRQGFsg2y7HjwNExEcYzzgdcZONai3otol8EaW7HJwnfIWUKtRHC0by_6Axayg7i9T3Yice16LOjHOr3RlIdhxBfl_kppI7Zrzg3Mk_2kDdeuOrvyjMnw/s1364/Screenshot%202024-03-12%20at%2012.30.35%E2%80%AFPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="724" data-original-width="1364" height="296" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhyxYpzmWN-tpl0LxNLefuCTyDQBWJB-6zhHZxqf7odLrwSn7AfjqgYoeT_AThr0sdtuefWFqRQGFsg2y7HjwNExEcYzzgdcZONai3otol8EaW7HJwnfIWUKtRHC0by_6Axayg7i9T3Yice16LOjHOr3RlIdhxBfl_kppI7Zrzg3Mk_2kDdeuOrvyjMnw/w558-h296/Screenshot%202024-03-12%20at%2012.30.35%E2%80%AFPM.png" width="558" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div>Okay....y'all. Are you ready for ABSOLUTE SINGLE MOLECULE SENSITIVITY?<p></p><p>Are you willing to accept 2 SCANS/MINUTE to get it?</p><p>No?!?!? </p><p>Why? Oh. You have multiple studies you'd like to complete before you retire? </p><p><a href="https://www.nature.com/articles/s41592-024-02207-8">Well.....crap....here it is anyway!</a> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQLiPlxxpHMXxGQ9YJ7xj37jSlz9mf2V0fUvpf9yGqLuMwOjMvee7jJusEuo7Pm-OIm2bUoEhscfGRbIotZK0U4hO2sank9-Ic3hKce4g-HGqzBZ-t7cce0U-jr7ecB5CxG9JUJziHFQRYS3rnB0LCZL1zyeHmSUcFcOIKwKx2-WsX1TMJ_phhZMPAWt8/s797/Screenshot%202024-03-12%20at%2012.32.37%E2%80%AFPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="497" data-original-width="797" height="318" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQLiPlxxpHMXxGQ9YJ7xj37jSlz9mf2V0fUvpf9yGqLuMwOjMvee7jJusEuo7Pm-OIm2bUoEhscfGRbIotZK0U4hO2sank9-Ic3hKce4g-HGqzBZ-t7cce0U-jr7ecB5CxG9JUJziHFQRYS3rnB0LCZL1zyeHmSUcFcOIKwKx2-WsX1TMJ_phhZMPAWt8/w509-h318/Screenshot%202024-03-12%20at%2012.32.37%E2%80%AFPM.png" width="509" /></a></div><br /><p>Look, there isn't enough helium left on earth for unimportant things like cooling large magnetic drivn FTMS systems which...could...well.... do this...ummm....same thing....?...at higher resolution and 50x faster....? We need the remaining helium on earth for MRI scanners, which are actually important. Now....how the "Everything costs $1" store my kid loves can seemingly fill seven thousand Helium balloons a day...for $1....is still a complete and total mystery to me. </p><p>Obviously, measuring a "single-ion" of anything is really really cool and not everyone's first motivation is how many chromatographic peaks across a scan they can get. Honestly, the most impressive part is probably the fact that "singe ion" didn't degrade in 25 seconds while making 400 zillion rotations around the inside of that little tiny vacuum chamber! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-37702388576998710022024-03-09T12:46:00.000-08:002024-03-11T12:50:43.037-07:00Need more surfactants for proteomics? Here is a big table! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEieAVdabxZAmkQraDpOoREBIvJhhPeIPAoDH-KdDJsZBN-_l9ox3g1fROw4D0e45HnlXbitFaasM3C5EFR7Ix2BsnCV7Z_LgGd9305At6NZuqCPgu1xOfVWlWpDBGvIS8J-qHB-rZxhCqN-fUFvB8mW-i2lkhOpz7chUV610t1c4HA4NXZGXTYnje1gAs0" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="655" data-original-width="872" height="382" src="https://blogger.googleusercontent.com/img/a/AVvXsEieAVdabxZAmkQraDpOoREBIvJhhPeIPAoDH-KdDJsZBN-_l9ox3g1fROw4D0e45HnlXbitFaasM3C5EFR7Ix2BsnCV7Z_LgGd9305At6NZuqCPgu1xOfVWlWpDBGvIS8J-qHB-rZxhCqN-fUFvB8mW-i2lkhOpz7chUV610t1c4HA4NXZGXTYnje1gAs0=w510-h382" width="510" /></a></div><br /><p></p><p>Okay, well, that looks grainy and useless, but if you are one of those "low sample input" people, you might also be looking for surfactant ideas! </p><p>We've all clustered around DDM because (so far, knock on wood) it doesn't seem to destroy everything. Longitudinal data would be nice and those of us using it to coat a lot of things will probably have some of that soon.</p><p>BUT THERE ARE MORE!<a href="https://www.mcponline.org/article/S1535-9476(24)00035-5/fulltext"> And you can read about them in MCP here!</a></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgBtk6zeJ30ZAwSlRVkw7qWY_hgHLIv5UP7zWYUaoS1s6Zuv1FLj_M-X4A-CBiJpk-fbx10J9ew_oSGDL4WumYTSlReyd1zq5b3K-A-N34RIhjOj96vJTsTjz2HFB5NSsKvt_qb3BxPw39DGhfxbbLLv6s-334EV2YHC2_-S3-dV9DCu2SNbrqnbd-oI-g" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="442" data-original-width="834" height="248" src="https://blogger.googleusercontent.com/img/a/AVvXsEgBtk6zeJ30ZAwSlRVkw7qWY_hgHLIv5UP7zWYUaoS1s6Zuv1FLj_M-X4A-CBiJpk-fbx10J9ew_oSGDL4WumYTSlReyd1zq5b3K-A-N34RIhjOj96vJTsTjz2HFB5NSsKvt_qb3BxPw39DGhfxbbLLv6s-334EV2YHC2_-S3-dV9DCu2SNbrqnbd-oI-g=w466-h248" width="466" /></a></div><br />They seem to have one they like better than DDM, but they have to remove it from the peptides afterward, which....is less immediately interesting to me personally....<p></p><p>but I sure am glad to have a whole table of things to try! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-11048069872056406262024-03-05T11:57:00.000-08:002024-03-10T12:00:03.373-07:00Is it time for cheaper, faster alternative enzymes for shotgun proteomics? <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhsKfW_G0sjkB7DfI_ZRrvQcMuP7SYosmYCvNI6rHDi-zDTVugmnItRZhwPHb8Tk7OBBYEXBwh8DfItic8ggnyZB57xPDOWvzxgYbMjex7JFBPXy9G4wVPMV4zy8lsTlgBLJH2qvFLwpjYbe6EyxuRjpOVNqBWqvCmqBkFslywOtsyjQFW_e8a7lq3nSTs" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="500" data-original-width="498" height="381" src="https://blogger.googleusercontent.com/img/a/AVvXsEhsKfW_G0sjkB7DfI_ZRrvQcMuP7SYosmYCvNI6rHDi-zDTVugmnItRZhwPHb8Tk7OBBYEXBwh8DfItic8ggnyZB57xPDOWvzxgYbMjex7JFBPXy9G4wVPMV4zy8lsTlgBLJH2qvFLwpjYbe6EyxuRjpOVNqBWqvCmqBkFslywOtsyjQFW_e8a7lq3nSTs=w379-h381" width="379" /></a></div><br /><p></p><p>Moving fast, but subtilysin ripping through intact proteins in seconds isn't the worst idea I've ever heard.</p><p><a href="https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00852">Strongly recommend you check this one out! </a></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjlyB_QkOs6KhV00GnJ5sIjQbBgYiXkczyUUVkSpR9l_Wd9-XtkwCUs6nm5S9S2VT5b3v5nlGvA3hzkYcCXvrRSMxrbELFD44G2IieckLTPd8g-2b3SvwSumLeBYoadFXpZiSPkAPUNC-KVXJc6WvOxoAMCEkIXQHOu2UKZ-IbAT7lO31vdJbxB9qxiS2g" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="333" data-original-width="878" height="199" src="https://blogger.googleusercontent.com/img/a/AVvXsEjlyB_QkOs6KhV00GnJ5sIjQbBgYiXkczyUUVkSpR9l_Wd9-XtkwCUs6nm5S9S2VT5b3v5nlGvA3hzkYcCXvrRSMxrbELFD44G2IieckLTPd8g-2b3SvwSumLeBYoadFXpZiSPkAPUNC-KVXJc6WvOxoAMCEkIXQHOu2UKZ-IbAT7lO31vdJbxB9qxiS2g=w526-h199" width="526" /></a></div><br /><br /><p></p>LCMSmethodAdminhttp://www.blogger.com/profile/08617632260397675300noreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-76905316690162974132024-03-04T11:45:00.000-08:002024-03-04T11:45:07.176-08:00My alma mater ended a deal with Google - blog functionality impacted! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEj2eZEuc98tjtiuihT60WCVtfE8o7tPf_XzShJrnTIkfX2104OwvjaH6uk0ggp_nCCP9FoiLZPHr5uPQHIM2bAPnTUhnW2BpfDqvU4mxq0b3TJhxV4g_j_p8ETj1laHft7TxXLPTZAaWTvgKvEay2mhsce1CbXP3mBiasW1Mlb3ThPnaFNjXD0_1Xc57dI" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="145" data-original-width="227" height="204" src="https://blogger.googleusercontent.com/img/a/AVvXsEj2eZEuc98tjtiuihT60WCVtfE8o7tPf_XzShJrnTIkfX2104OwvjaH6uk0ggp_nCCP9FoiLZPHr5uPQHIM2bAPnTUhnW2BpfDqvU4mxq0b3TJhxV4g_j_p8ETj1laHft7TxXLPTZAaWTvgKvEay2mhsce1CbXP3mBiasW1Mlb3ThPnaFNjXD0_1Xc57dI" width="320" /></a></div>So.... short story is that Google and Virginia Tech had a long standing deal to work together. However, Google wants money for things these days and my alma mater was like - ummm....we'll go to the amazing people at Microsoft if we have to pay money.... cause.... outlook is clearly almost 1% as good as Gmail....<p></p><p>So....I need to migrate 140GB of data by tomorrow night to somewhere.....</p><p>Many blog links leading to my Google Drive are already down (ugh). This includes any historic methods on www.LCMSmethods.org that haven't been migrated successfully to protocols.io</p><p>I'm unclear what happens to the other 138GB of pictures and .gifs that are linked to this site. LMAO. DO YOU KNOW HOW LONG IT TOOK ME TO DOWNLOAD 138 GB OF GIFS?<br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-67679117876593020632024-03-03T03:28:00.000-08:002024-03-03T05:59:43.461-08:00Veneer -- identify the real cell surface proteins! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiA6JJr3fDnLZWgCk0_6y6pZPZjjgXpsmTRAW_ruPujMvxIW19QO-7U4clDRdG9w-PhRAClBO25E9O9ZByjV3R7lGsB-Fk7KKeL3WWzFbVh0yOhJYNTgjV_7upp7w2y8RSh5_7rBPI5tG4IexN31vq5svhei69KE1_smCbDJ2HxIiSQehsxsOs-RUPNsno" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="261" data-original-width="500" height="263" src="https://blogger.googleusercontent.com/img/a/AVvXsEiA6JJr3fDnLZWgCk0_6y6pZPZjjgXpsmTRAW_ruPujMvxIW19QO-7U4clDRdG9w-PhRAClBO25E9O9ZByjV3R7lGsB-Fk7KKeL3WWzFbVh0yOhJYNTgjV_7upp7w2y8RSh5_7rBPI5tG4IexN31vq5svhei69KE1_smCbDJ2HxIiSQehsxsOs-RUPNsno=w503-h263" width="503" /></a></div><br /><p></p><p>Is that a cell surface protein? Oh yeah, sure it is, someone in 2003 BLAST'ed the genome sequence for it and found a yeast cell surface protein with 12% sequence homology....</p><p>And....that may honestly summarize some percentage of "cell surface proteins" we have on our lists. Legitimately somewhat informed guesswork based on organisms separated in evolution over 1.5 billion years. Or something.</p><p>Of course people have built off of these guesses by raising antibodies and verifying by microscopy, etc., but we have never had an easy way to rapidly annotate mammalian proteins as truly being on the cell surface.</p><p><a href="https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00800">UNTIL NOW. Introducing Veneer</a>!</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZzgewN8l4V5HaSg6OA-TGmjmL6KrGHImN5IPrCpEmB8hykg-TZ_1Ek9rFYsLTREaXE90v9-v0n-dzHxNDQzu0eDw6UYl3_GxqhSZ-IIWzH76BGy6QPXNHu2WxAVE0oWivigxoPYw-_EVWQOCtVbtnCb3cXu2MIsN69933CYhJixUxRVEBK-E1TOZTmes/s1088/Screenshot%202024-03-03%20at%206.05.05%E2%80%AFAM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="396" data-original-width="1088" height="186" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZzgewN8l4V5HaSg6OA-TGmjmL6KrGHImN5IPrCpEmB8hykg-TZ_1Ek9rFYsLTREaXE90v9-v0n-dzHxNDQzu0eDw6UYl3_GxqhSZ-IIWzH76BGy6QPXNHu2WxAVE0oWivigxoPYw-_EVWQOCtVbtnCb3cXu2MIsN69933CYhJixUxRVEBK-E1TOZTmes/w514-h186/Screenshot%202024-03-03%20at%206.05.05%E2%80%AFAM.png" width="514" /></a></div><br /><p>There is a lot to unpack in this great new resource. The background of the resource was constructred from data from over 4,000 separate publications! </p><p>"There are many different ways to enrich cell surface proteomes, I bet this only thinks about the one this group uses"</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3vestYj7gCheBGrCTMrTZBa5B-5vJg_XtMdWh1BuXPnYYJVN2Hf5dlxZIt-0dOhUGb9tgF52SFo3FKZnCHHTHMV2461XWMh266tWFPnqH-hZTGL1qWzoLuGkZgBah96RrNuMC4CwloXNCqCdGDMAM4fDyqtEEDEdGT4FspKB82pCFtbsj0j0JoZV9l-Q/s220/false-wrong.gif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="220" data-original-width="220" height="220" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3vestYj7gCheBGrCTMrTZBa5B-5vJg_XtMdWh1BuXPnYYJVN2Hf5dlxZIt-0dOhUGb9tgF52SFo3FKZnCHHTHMV2461XWMh266tWFPnqH-hZTGL1qWzoLuGkZgBah96RrNuMC4CwloXNCqCdGDMAM4fDyqtEEDEdGT4FspKB82pCFtbsj0j0JoZV9l-Q/s1600/false-wrong.gif" width="220" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFSlvmjwBdbu_EPBiqXh9eUHca75Br6k9Jd0R5NsqBwfMdCN-wT7BoOD3HxE_DBdaWCGRdrgBtaw5dHw2IcOYirbgDVEueB7O1cWAf4NpoAK_dmU8IPMWCwM1hjUN4y391NBtTSsg4ejM6olXn3NlItMh7P9JPE-SQ8BI4uLUrDsAckyiCohfZOFXcglk/s2230/Screenshot%202024-03-03%20at%206.15.26%E2%80%AFAM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1448" data-original-width="2230" height="377" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFSlvmjwBdbu_EPBiqXh9eUHca75Br6k9Jd0R5NsqBwfMdCN-wT7BoOD3HxE_DBdaWCGRdrgBtaw5dHw2IcOYirbgDVEueB7O1cWAf4NpoAK_dmU8IPMWCwM1hjUN4y391NBtTSsg4ejM6olXn3NlItMh7P9JPE-SQ8BI4uLUrDsAckyiCohfZOFXcglk/w580-h377/Screenshot%202024-03-03%20at%206.15.26%E2%80%AFAM.png" width="580" /></a></div><br /><p>Shown here are the Veneer processed results from 4 separate enrichment methods! </p><p>It doesn't take much imagination to think what Veneer could do for the biology community, right? I've never made an antibody before but my impression of it is that it is 1) expensive 2) takes forever and 3) requires you to go all vampire on 700 bunny rabbits, 11 camels and possibly 1.5 cheetahs. If you need to make a cell surface antibody and that protein really isn't a cell surface protein OR you are raising the antibody to a a section of that protein that is not actually the part ON THE CELL SURFACE. That's a lot of bunny / camel /cheetah blood for ....absolutely.....nothing...... </p><p>Vaneer doesn't have to be perfect to have a major effect on efficiency. Anything would help drastically but they obviously put loads of thought into this amazing new resource. If you're swamped for time, you don't even have to read this paper. Check out the logic summarized in Figures 2 and 4. </p><p><a href="https://github.com/GundryLab/veneer">Or just download Veneer from this Github and run it</a> (might be a minor UTF-8 issue for Macs) now!</p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-79579460107947508242024-03-02T15:03:00.000-08:002024-03-02T15:03:31.435-08:00The long overdue midiaPASEF post! <p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFcX889m_ZHYBm_l-SxsT5yFmhDHj8bNlmDI-plyKsnrrSRXlW_4NhUgwrnFZGT6UzQnbwJOf48GNjX2D59nnZk8aRReB81_KPEmyxtK6ZxgT8p8s1Ap34mA8xEfbvpv2DebG_aVk60n_7QTWAtVY0i_NJKp9b61QikzreDDngbjg3oteGZuCGGqW4K-A/s1156/Screenshot%202024-03-02%20at%205.27.52%E2%80%AFPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="994" data-original-width="1156" height="492" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFcX889m_ZHYBm_l-SxsT5yFmhDHj8bNlmDI-plyKsnrrSRXlW_4NhUgwrnFZGT6UzQnbwJOf48GNjX2D59nnZk8aRReB81_KPEmyxtK6ZxgT8p8s1Ap34mA8xEfbvpv2DebG_aVk60n_7QTWAtVY0i_NJKp9b61QikzreDDngbjg3oteGZuCGGqW4K-A/w572-h492/Screenshot%202024-03-02%20at%205.27.52%E2%80%AFPM.png" width="572" /></a></div><p>Almost a year ago I tried to figure out <a href="https://proteomicsnews.blogspot.com/2023/05/diapasef-what-are-all-these-new-methods.html">"all of these diaPASEF methods and what they do"</a> and one of the most innovative ones didn't make the list. Maybe I posted<a href="https://www.biorxiv.org/content/10.1101/2023.01.30.526204v1"> the preprint link</a>, but I honestly couldn't figure out what the Albert Heck they were even typing about. </p><p>Today, thanks to the fact everyone in my house has been sick for an entire month I got to sit through a talk by Stefan Tenzer that is posted on YouTube, but you can only get the link for it <a href="https://bruker-marketing.actonsoftware.com/acton/form/4047/03f3:d-0001/0/-/-/-/-/index.htm">by registering here.</a> </p><p>My motivation was something called VistaScan that is now available on some/most(?) TIMSTOFs if you have TIMSControl 5 or higher. VistaScan is related to midiaPASEF, but on a limited scale. </p><p>My real motivation was trying to make VistaScan do something I want it to do that I can now say with absolute certainty that midiaPASEF can not do, nor will it ever be able to do it. Instead of being bitter about an hour of my life I will never ever get back (the video is shorter than that I had to stop and think about things and back up several times), I'm legitimately really happy to understand the concept. </p><p>Like the other diaPASEF methods, this one leverages the very handy properties of being able to discriminate peptides by retention time, ion mobility and accurate mass. What sets this one apart is that the quadrupole (the fastest part) is moving in overlapping windows. Obviously, not new stuff, and this method was inspired by MacCoss lab's multiplexed PRM stuff that is so smart that no one aside from the authors have ever been smart enough to use it themselves. </p><p>While on the surface you can look at the midiaPASEF posters and technical notes from the vendor and think - "okay, they're doing tiny window DIA while leveraging ion mobility" (okay, that's what I thought). It's not quite that. It is still using relatively large mass isolation windows, but because they're overlapping and the data acquisition is very very fast, they can deconvolute the data (again, similar to multiplexing PRMs). </p><p>The trick, then, is on the software side, where the data needs to be modeled over the sliding windows. If, for example, you see your precursor fall off as the quad slides past a certain point, then you know the upper mass range of that precursor. Where this gets really smart is that they also have to track the fragment ions the same way. </p><p>Your diaPASEF window is still loaded with fragments from everything within the 12 Th (or 16 Th, I forget) window, but by modeling the fragments that disappear as you tick the isolation window up or down, you can start to extract the fragments that correspond with that exact precursor.</p><p>You get the added benefit on top that you are altering the TIMS isolation as well. Where this becomes contrary to my motivations was that I was simply hoping to do the 2Da window overlapping DIA stuff that I was doing for SCoPE-MS on the ZenoTOF with an extra dimension - ion mobility.</p><p>But if I'm tracking reporter ions which are present in every MS2 scan, then these can't be modeled. It is definitely possible, however, <a href="https://proteomicsnews.blogspot.com/2017/10/tmt-c-simple-method-to-improve-ms2.html">to use the complementary ion pair</a>s, but to process those data you've either got to have Thermo .RAW or have access to that super mysterious data processing server that has those capabilities. Neither of which match here. </p><p>Doesn't work for my application, but it's still super cool. Where I have a disconnect is the VistaScan thing which appears to be a limited version of midiaPASEF that only works for some applications. I'm hoping to test some things on it (just got a 5.0 upgrade) and I suspect that we can generate the data but not process much of it. We'll see though! </p><p><br /></p><p><br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-39628248999264734142024-02-27T06:28:00.000-08:002024-02-27T06:28:21.207-08:00Insights into proteomics in 2024 from blog traffic numbers! <p>The dashboard of this blog gives me interesting insights at times. I get easy metrics for what posts people (completely anonymous) engage with. And where (geographically) traffic is coming from as well as some insights into what links people are coming from, to some degree. Like when Twitter had a lot of functional features I could tell that people were coming from Twitter links that were posted. None of that works since...well....you know....</p><p>While I've got 2 hours of sleep because one of those adorable little germ factories gave my adorable little germ factory the worst virus of his entire life, I thought I'd summarize some of what I see when I log in because I don't have enough sleep to remember what I was actually planning to do. </p><p>Insight #1: If I want to decrease traffic, write about single cell proteomics (SCP)</p><p>While the outside world really seems to care about SCP, while still being largely confused about what it is, who is doing it, and why the scSeq core can't help them with it, my small reader base is not interested in today's newest advance. Since I have been personally interested, this has directly hurt blog viewership numbers. For real, we're talking crushing readership numbers. The only thing worse is to write about Metabolomics. </p><p>Insight #2: If I want to attention post a tutorial or talk about a "next gen" proteomics technology</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMtbDsDCWXVznZWCj95lwh6wxygVKBqgE3HQ44w1Kn_llfzMU-k7DDgFuODoswApfkbD-sDpP8cc3DEovXhVPkSfhZzEMniWP8YlvucH9HuPYaSOd0wPUm_7kiH-JZGP330cxNfazutNmVS6F6Yk8NAgw5yCz0TQkbesGx5tchGZ6xuvCkt8M-B33h-3k/s984/SomaScanInsights.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="131" data-original-width="984" height="90" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMtbDsDCWXVznZWCj95lwh6wxygVKBqgE3HQ44w1Kn_llfzMU-k7DDgFuODoswApfkbD-sDpP8cc3DEovXhVPkSfhZzEMniWP8YlvucH9HuPYaSOd0wPUm_7kiH-JZGP330cxNfazutNmVS6F6Yk8NAgw5yCz0TQkbesGx5tchGZ6xuvCkt8M-B33h-3k/w668-h90/SomaScanInsights.JPG" width="668" /></a></div><br /><div class="separator" style="clear: both; text-align: left;">Here are a couple examples of posts with recent traffic metrics. These are between 4 and 10x more traffic than any recent SCP post. Highlighting SomaScan's ....trepidation....for actual quantitative comparisons and how MS1 libraries work. </div><br /><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMHgYgL7NRjRKPBFijdggSuXBLihjX3txzWLpNIbNzCoZ_FkVChh_7qV8q1zEtpY-i8yUuXqggWTNr6hZoDEiZCTPhY_7iEYi-e6mNmtUC9j2grOBOsDxlZvBQWBlVpasGlDMoEj336VBsp_oYqFnDxSOnnDyN-rtj0QrAhcF_fehNMrF5MLvP06KwzDs/s989/NanoPoreProteomics.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="127" data-original-width="989" height="84" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMHgYgL7NRjRKPBFijdggSuXBLihjX3txzWLpNIbNzCoZ_FkVChh_7qV8q1zEtpY-i8yUuXqggWTNr6hZoDEiZCTPhY_7iEYi-e6mNmtUC9j2grOBOsDxlZvBQWBlVpasGlDMoEj336VBsp_oYqFnDxSOnnDyN-rtj0QrAhcF_fehNMrF5MLvP06KwzDs/w662-h84/NanoPoreProteomics.JPG" width="662" /></a></div><br /><div>Same here, recent post where that group forced one protein through a NanoPore and just a simple tutorial (thanks to Ed Emmott's lab making an XML) for how to process data that was not -at the time -natively compatible with MaxQuant (I'm sure it is now). Big engagement numbers relative to other posts.</div><div><br /></div><div>Insight #3: - The big one - People really need very basic help with proteomics. Check out the recent traffic to some of these permanent pages!</div><div><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEia9NBnDDPZMjHLQVIrFqhXuGUWhwapKhqfSQHhnHdtuoE5LyxgAI6-_SgSUYIaHx231q7i7OPaRIHHC5-NC3kcdilmHgTjCIzaCh4jLoPDDZPQ1TlFKgQhhNjjo241bMzhNZ_1mwPSWm90kFNNuYrFs09JHMAT92vqggEzU__uIhi5bREBwuj4CYdrTv4/s1035/HelpPages.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="850" data-original-width="1035" height="443" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEia9NBnDDPZMjHLQVIrFqhXuGUWhwapKhqfSQHhnHdtuoE5LyxgAI6-_SgSUYIaHx231q7i7OPaRIHHC5-NC3kcdilmHgTjCIzaCh4jLoPDDZPQ1TlFKgQhhNjjo241bMzhNZ_1mwPSWm90kFNNuYrFs09JHMAT92vqggEzU__uIhi5bREBwuj4CYdrTv4/w539-h443/HelpPages.JPG" width="539" /></a></div><br /><div>The "terminology translator" has always been a major draw to the blog. "What is this weird acronym the guy in the basement used that I don't know?" But "what is proteomics" still gets a lot of hits even though I made a long drawn out analogy about a car I was obsessed with when I was a kid. And both "resources for newbies" and "now I have a protein list" get slammed with new traffic, which makes me realize how important it is that I update these once in a while. I'm sure I'll physically cringe when I see how old some of the links in those posts/pages are. </div><div><br /></div><div>We see this exact same thing with r/proteomics, though most of the stuff appears to go to r/massspectrometry or r/bioinformatics first. A lot of the traffic is "how do I process these data in DIA-NN". "What does this q-value thing mean?" </div><div><br /></div><div>This is all good stuff, I think. It means that new people are engaging with proteomics technology. And -- since you still can't get a degree (though many European schools have formal coursework in mass spectrometry and proteomics) people need help with these things. The bad news is that they might just be Googling it and ending up at a site maintained by someone who has less time to put into it every year. </div><div><br /></div><div><u>If you are generating high quality freely/openly available content to help people new to proteomics please reach out so I can direct people your way!</u> </div>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-52764242118181617642024-02-26T05:41:00.000-08:002024-02-27T05:53:42.077-08:00More amazing archaeology proteomics - sex determination from teeth?!?!<p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPFFAd3Pzl_DeCjN-FH1bDUNitLd-KHEin6Gq89ofh4GCw0uNF6Q9jQd3IILDAbAkwJRciU0Zf5TVbXbNMxxafDAqNMi_x2MpCIFyypGjzoQVDNE7abD2wpqtsIVZNSO2ebaAORil85Hpl3Fp-sMgfPIK3OOAYIhgyCF8tNV49AdTB4ay_6jCP4MhHK9k/s624/TeethSexdeterminationProteomics.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="427" data-original-width="624" height="334" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPFFAd3Pzl_DeCjN-FH1bDUNitLd-KHEin6Gq89ofh4GCw0uNF6Q9jQd3IILDAbAkwJRciU0Zf5TVbXbNMxxafDAqNMi_x2MpCIFyypGjzoQVDNE7abD2wpqtsIVZNSO2ebaAORil85Hpl3Fp-sMgfPIK3OOAYIhgyCF8tNV49AdTB4ay_6jCP4MhHK9k/w488-h334/TeethSexdeterminationProteomics.JPG" width="488" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div>Rapidly climbing the list of "who I want to be when I grow up" thanks to <i>a diffuse and seemingly unfocused</i> series of paradigm shifting studies is one Jesper V. Olsen. (Words in italics are from one of my favorite recent podcasts we recorded) <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAnnD-f-YavRwzbcg4Q-L9pWvaDDbiJpYRS1KZYk3DUjtBxuHKGnsLFCSHfkP1U2_wDpG9HBzG9ZIRxB1Zphdy3Glrz11UkHb_XS-y8NsnZDnGuLmyiT4sw8pdZLeOei2ZT3W2ABT-B1nGydbTxY3c7OZ50jHWqT4t5HJ03CpZlkI7oujMhYN5HVgFAM4/s649/SexDeterminationProteomicsTeethBiorxiv.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="455" data-original-width="649" height="367" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAnnD-f-YavRwzbcg4Q-L9pWvaDDbiJpYRS1KZYk3DUjtBxuHKGnsLFCSHfkP1U2_wDpG9HBzG9ZIRxB1Zphdy3Glrz11UkHb_XS-y8NsnZDnGuLmyiT4sw8pdZLeOei2ZT3W2ABT-B1nGydbTxY3c7OZ50jHWqT4t5HJ03CpZlkI7oujMhYN5HVgFAM4/w525-h367/SexDeterminationProteomicsTeethBiorxiv.JPG" width="525" /></a></div><div><br /></div><a href="https://www.biorxiv.org/content/10.1101/2024.02.20.581140v1">It isn't that diffuse because Olsen lab has been doing some amazing stuff pushing the boundaries of what we thought we could do with archaeological samples - with proteomics</a>. But when you look at the amazing disease work on top it's easy to think they're all over the place. As a whole it's just amazing lines of productivity in multiple directions. Does that justify the 2 invertebrate studies we've written and haven't submitted yet because I'm trying to build a coherent theme to my CV? Meh. I guess we'll see. <div><br /></div><div>When you find human archaeological samples you can tell sex if they are very very well preserved. Which is also very very rare. Teeth, however, are really tough. So....if you want sex information from these materials you can guess... or you can use laser etching to get down to proteins <a href="https://github.com/ClaireKoenig/SexIdentification">in teeth and do PRMs and then load your data into this Shiny interface and</a>....now you know for sure....</div><div><br /></div><div>RIGHT?!?!?! <br /><p><br /></p></div>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-48411733389258194912024-02-24T03:15:00.000-08:002024-02-24T05:36:46.812-08:00We're out of the backwater! <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKR1h3KHT3tk4I1diGB4kvefmK6lB2rURxO-0yo0rIJkJM7sVNlowsArpekOBYAIltCfkZqHN6MyxUzyGjU0FgyobFQTeovlATRdgElvJXnkzRisaKRw-LY5xq30Trf6P7syTWFc_Qjpbgf3XVoyqp54FASiAWSVlEv8SLIuRjZh4Ui-iYOGPaWQz2DIQ/s1902/Screenshot%202024-02-24%20at%205.49.46%E2%80%AFAM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1902" data-original-width="1852" height="522" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKR1h3KHT3tk4I1diGB4kvefmK6lB2rURxO-0yo0rIJkJM7sVNlowsArpekOBYAIltCfkZqHN6MyxUzyGjU0FgyobFQTeovlATRdgElvJXnkzRisaKRw-LY5xq30Trf6P7syTWFc_Qjpbgf3XVoyqp54FASiAWSVlEv8SLIuRjZh4Ui-iYOGPaWQz2DIQ/w509-h522/Screenshot%202024-02-24%20at%205.49.46%E2%80%AFAM.png" width="509" /></a></div><br /><br /><p></p><p>I'll probably be backdating some posts. I've been busy busy busy, but I haven't slipped far from my reading a paper every day rule, its just finding time to summarize and post them here. </p><p>Need some motivation to get back at it? How 'bout us cracking another big industry magazine?</p><p><a href="https://endpts.com/once-a-scientific-backwater-protein-research-attracts-billion-dollar-deals-and-high-profile-publications/">You can check it out here. </a> (Shoutout to Dr. Luke Gamon for the heads up on this!) </p><p>Okay...so I was thinking about what backwater was and it reminded me of an old Saturday morning cartoon show. Surprisingly, Google could figure out what I was thinking about.....</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaoPJ7Sk2s02h1-RKYbQ5Jpsqkc6g9YmWrNykys-qHBUE5nb1UIFevZiEqWbw7a_ByDexDabdi5twUBWQeN4dJN1CEpYJx_bEhJQlcGd_U11gTeSxA94EENDP1Tjy6wm9J3JTuobEpNUZysTGV26MIy-PMBIzNInhqT87O7RAiNKJbvin4URwqFnPxgAI/s994/Screenshot%202024-02-24%20at%208.35.19%E2%80%AFAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="994" data-original-width="830" height="435" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaoPJ7Sk2s02h1-RKYbQ5Jpsqkc6g9YmWrNykys-qHBUE5nb1UIFevZiEqWbw7a_ByDexDabdi5twUBWQeN4dJN1CEpYJx_bEhJQlcGd_U11gTeSxA94EENDP1Tjy6wm9J3JTuobEpNUZysTGV26MIy-PMBIzNInhqT87O7RAiNKJbvin4URwqFnPxgAI/w363-h435/Screenshot%202024-02-24%20at%208.35.19%E2%80%AFAM.png" width="363" /></a></div><br /><p><br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-51301920600890361052024-02-23T03:17:00.000-08:002024-02-24T03:20:11.541-08:00FeMS - Navigate those career transitions! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEg7B_k_nj-Qbqc_f2VL13nz9eZncRDDCKhjbKFm3Cq1OtgVxovc-C96QiVC1wK-nRbJUCl2PRv-Cw7A7yYoOBU0eEJEdmIIfzxrvWmVRDG4UR0czIsU3TOo-6v0Wxxdsl6hh-LWdkzVaD1kwW5TSQESHiIy1_JlRbG_oXaSgou8B6yw1rW6u5UPvXsmxxE" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1080" data-original-width="1080" height="459" src="https://blogger.googleusercontent.com/img/a/AVvXsEg7B_k_nj-Qbqc_f2VL13nz9eZncRDDCKhjbKFm3Cq1OtgVxovc-C96QiVC1wK-nRbJUCl2PRv-Cw7A7yYoOBU0eEJEdmIIfzxrvWmVRDG4UR0czIsU3TOo-6v0Wxxdsl6hh-LWdkzVaD1kwW5TSQESHiIy1_JlRbG_oXaSgou8B6yw1rW6u5UPvXsmxxE=w459-h459" width="459" /></a></div><br /><p></p><p>The great Females in Mass Spectrometry organization is holding an awesome panel discussion at US HUPO on 3/10! Look at that lineup and career stage pacing. </p><p>Can't make it? <a href="https://femalesinms.com/">FeMS has tons of great content all the time! You can find out what they're up to here.</a></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-1673478797426726982024-02-22T03:25:00.000-08:002024-02-24T03:32:14.716-08:00Phosphopeptide retention time prediction numbers! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiXxOLbKiChRhMhRuAy3RsW4Cg-6lZSQ3s2p_cbF-MvLuHctt7ezvASGS0PcIO1U4r6Tq4fvKEEdFG9F1ESBxch4oR_9i-y8WJHVLU1Bkhlj3YYf3EkJ1HHaSUPxoj28VTirURJLGs6mI5R3yHcqEc0hcQ1ipLNwuaPUTOGNRJJ8tpZesEMT8lsByFjNCo" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="537" data-original-width="586" height="426" src="https://blogger.googleusercontent.com/img/a/AVvXsEiXxOLbKiChRhMhRuAy3RsW4Cg-6lZSQ3s2p_cbF-MvLuHctt7ezvASGS0PcIO1U4r6Tq4fvKEEdFG9F1ESBxch4oR_9i-y8WJHVLU1Bkhlj3YYf3EkJ1HHaSUPxoj28VTirURJLGs6mI5R3yHcqEc0hcQ1ipLNwuaPUTOGNRJJ8tpZesEMT8lsByFjNCo=w465-h426" width="465" /></a></div><br /><p></p><p>We all know phosphorylated a peptide changes the retention time. How much, though? And how much does changing the brand/type of C-18 resin change that shift? (<a href="https://www.sciencedirect.com/science/article/pii/S0021967324000876?casa_token=FXmvM3jHdFAAAAAA:UAfaMjJD_R9nJwltic7O-M-6WAHnsz4EpSaXeoSQm9-Xi1UGwRufbfuhNotSTDUVPt1wOso#fig0002">Where this study really shines!). </a></p><p><a href="https://www.sciencedirect.com/science/article/pii/S0021967324000876?casa_token=FXmvM3jHdFAAAAAA:UAfaMjJD_R9nJwltic7O-M-6WAHnsz4EpSaXeoSQm9-Xi1UGwRufbfuhNotSTDUVPt1wOso#fig0002">BOOOM! </a></p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgn1Ekn_9erR8HkaXj6b-20StIplR7JlTKUN4TCZxK_GA3_jLMEPwrCItUi5L2J6Uo2KetJF8a5HCU0IHdlkh1WC8-a8C7KM7oV639h-J4plcRAUtGPiJ5QmFzWBbbP9mPX6j_H2FvEB2ynHBDsbzP95WMEEVeQim25yxgbiuq4hkYUin0Oy9gpNeuh87A/s1396/Screenshot%202024-02-24%20at%206.29.11%E2%80%AFAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1156" data-original-width="1396" height="416" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgn1Ekn_9erR8HkaXj6b-20StIplR7JlTKUN4TCZxK_GA3_jLMEPwrCItUi5L2J6Uo2KetJF8a5HCU0IHdlkh1WC8-a8C7KM7oV639h-J4plcRAUtGPiJ5QmFzWBbbP9mPX6j_H2FvEB2ynHBDsbzP95WMEEVeQim25yxgbiuq4hkYUin0Oy9gpNeuh87A/w503-h416/Screenshot%202024-02-24%20at%206.29.11%E2%80%AFAM.png" width="503" /></a></div><br /><p><br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-62299000964783815522024-02-21T03:36:00.000-08:002024-02-24T03:45:59.448-08:00Ion mobility at 1,100 resolution with escalator ramping! <p> </p><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvDLk8iZHz5xXmJJE3OtPE0oriQWEd8Jou29iIK7YqYG5lLGNGoupN6BTJyDnCParlwfH-4_wAklGWBkUDOH3E9WyqkF69Qk5LsQU4Rwu_NceaTqon97IZgGbncvhVY0qT0X8fW-vRitjjRDPyTLA_xMoghwDZbFP22yR92DelMoDxeTJTO9fRSG_eVqw/s500/ac3c05594_0007.webp" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="269" data-original-width="500" height="316" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvDLk8iZHz5xXmJJE3OtPE0oriQWEd8Jou29iIK7YqYG5lLGNGoupN6BTJyDnCParlwfH-4_wAklGWBkUDOH3E9WyqkF69Qk5LsQU4Rwu_NceaTqon97IZgGbncvhVY0qT0X8fW-vRitjjRDPyTLA_xMoghwDZbFP22yR92DelMoDxeTJTO9fRSG_eVqw/w588-h316/ac3c05594_0007.webp" width="588" /></a></div><br /><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">Ion mobility is finally showing results to back up the promise we've been told it had for decades. People are doing amazing things with the aid of FAIMS. Most commercial units of that have resolutions around 10. </div><div class="separator" style="clear: both; text-align: left;">The TIMS thing that took Bruker selling 1 mass spectrometer every 3 years to someone who was either gullible or really needed an FTICR to ALMOST $1 BILLION IN REVENUE IN 2023 has a resolution around 100-200 depending on how you measure it.</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">You can get "gas phase NMR" for your Thermo instruments, which is a high resolution FAIMS from HeartStone that is in excess of 200 resolution.</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;"><a href="https://pubs.acs.org/doi/full/10.1021/acs.analchem.3c05594?casa_token=KOZtsVVT9hEAAAAA%3AXawQE1900xjwYxkAeV2fIzdnUna9TgcZI2azZGwPUexPztnZb6yvAT5K2VTmUGBPNSa7YkZjGoVkZg">But 1,000 resolution???? "Lossless"? If IMS is your thing, this is your paper!</a> </div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjleW5VaJAWLL_yKhjfCWzPMZ_PzCCyhAhqz4fYzKAQToaBFxKdnOSRc-JLs7XC0XAZZTfLatl8a_-vify4-BBKAf2ePJ-RB538UkTnBAwQylE0LdExHVOav3W6Yeb3cMvJdUhqHddqUqKis1t7F0iDgYLQ_hhchLM4tk2xHB00vPw7umw5Yho4Vu3lfYs/s2454/Screenshot%202024-02-24%20at%206.44.56%E2%80%AFAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="656" data-original-width="2454" height="151" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjleW5VaJAWLL_yKhjfCWzPMZ_PzCCyhAhqz4fYzKAQToaBFxKdnOSRc-JLs7XC0XAZZTfLatl8a_-vify4-BBKAf2ePJ-RB538UkTnBAwQylE0LdExHVOav3W6Yeb3cMvJdUhqHddqUqKis1t7F0iDgYLQ_hhchLM4tk2xHB00vPw7umw5Yho4Vu3lfYs/w563-h151/Screenshot%202024-02-24%20at%206.44.56%E2%80%AFAM.png" width="563" /></a></div><br /><div class="separator" style="clear: both; text-align: left;"><br /></div><p></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-8726705580142021552024-02-12T02:42:00.000-08:002024-02-12T11:08:45.155-08:00Reflections on the EuBiC Winter School (Guest blogger post!) <p style="text-align: center;"><span id="docs-internal-guid-c4d99566-7fff-806b-ab12-4c13c4788e59"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; font-weight: 700; vertical-align: baseline; white-space-collapse: preserve;"><span style="border: none; display: inline-block; height: 268px; overflow: hidden; width: 602px;"><img height="268" src="https://lh7-us.googleusercontent.com/UpsOOqKNpkrDSlQS7q8L0bZnaEF5Kcex8M1NHuGmPtbI_DokmW4myBrVarqxVdqIRfELT-atsm2IDVgKNQahU0NLMnmu-C3lkvMgCZyrgIZbbHdxmP7itk0_WF063Im1-in3oKaw6Xh8Ee3bz_MHhUo" style="margin-left: 0px; margin-top: 0px;" width="602" /></span></span></span></p><h2 dir="ltr" style="line-height: 1.38; margin-bottom: 6pt; margin-top: 18pt;"><span id="docs-internal-guid-c4eee03f-7fff-7a32-448b-853c2ade3320" style="font-weight: normal;"><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">As the snow was not so gently falling on the charming town of Winterberg, Germany, the stage was set for the EuBIC-MS (</span><a href="https://eubic-ms.org/" style="text-decoration-line: none;"><span face="Arial, sans-serif" style="color: #1155cc; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; text-decoration-line: underline; text-decoration-skip-ink: none; vertical-align: baseline; white-space-collapse: preserve;">https://eubic-ms.org/</span></a><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">) Winter School 2024 - an engaging five-day conference dedicated to (computational) proteomics, mass spectrometry, and bioinformatics. The days were filled with keynote talks, workshops, and great scientific and non-scientific discussions! Since the first edition in 2017, this biennial event has brought together early-stage PhD students eager to step into computational proteomics and experts from the field.</span></p><br /><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">The conference set off with educational workshops arranged by us PhD students in the PROTrEIN (</span><a href="https://protrein.eu/" style="text-decoration-line: none;"><span face="Arial, sans-serif" style="color: #1155cc; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; text-decoration-line: underline; text-decoration-skip-ink: none; vertical-align: baseline; white-space-collapse: preserve;">https://protrein.eu/</span></a><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">) training network. We held several parallel workshops on mass spectrometry-based proteomics workflows, PTM identification, and prediction models. For us in PROTrEIN it was a great opportunity to arrange these workshops to really see how far we have come since the project started! In our kick-off back in September 2021 we were the ones attending similar workshops, and now, 2.5 years later we are grateful to have the opportunity to host such workshops. In parallel with our workshops, there were also workshops about demystifying GitHub actions and a workshop held by MSAID about analysis using their tool CHIMERYS. </span></p><br /><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Attendees would certainly agree that the poster session on Tuesday evening was particularly engaging. Young researchers from diverse backgrounds had the opportunity to showcase their latest work which led to many innovative and stimulating discussions. </span></p><br /><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Despite the flurry of academic sharing and learning, we did not lose sight of the fun. Ben & Ben (Orsburn & Neely) did a live recording of their podcast “The Proteomics Show” with a special guest from the audience! It was really interesting to see Ben & Ben in action and get behind the scenes a bit. Ben (Orsburn) also talked about his journey writing this blog - which gave us some insight into what it really entails. Wednesday concluded with a social event that saw us sledding down the snowy slopes of Winterberg, a fun and memorable experience that brought us all closer together. </span></p><br /><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">We must not forget to mention the 10 great keynote talks that covered diverse topics in the field. From isotopes to good practice of data sharing to single-cell proteomics and FASTA files of sealion proteomes. Many of the keynote speakers had also prepared workshops where the participants could dive deeper into the topics. </span></p><br /><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;">Looking back, the EuBIC-MS Winter School 2024 was more than just a conference. It was a gathering of a great community of people, a platform for learning and sharing, and a testament to the exciting developments in the field of proteomics, mass spectrometry and bioinformatics. Thanks to everyone who was part of the organizational team, all the keynote speakers, all the participants and to Ben for letting us use his platform to share about our experience at this event! </span></p><div><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><br /></span></div><div style="text-align: center;"><span face="Arial, sans-serif" style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline; white-space-collapse: preserve;"><span id="docs-internal-guid-5375614f-7fff-f9d5-4364-610a63f39596"><span style="font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; font-variant-position: normal; vertical-align: baseline;"><span style="border: none; display: inline-block; height: 339px; overflow: hidden; width: 602px;"><img height="339" src="https://lh7-us.googleusercontent.com/tTjZgAfJo4ma2ee4V3UdkGeXVzLOPmq_elVm6n6vxca-2asyedX4SGCpd37DoA1LvDvoBkMSUT5x2y-KqtIq3D-MUqHEK6PqUtgJbppbeWLzvnVlUC_x-s75sQ0VGEayncqDDuqugP6hMlgGkuEhhdQ" style="margin-left: 0px; margin-top: 0px;" width="602" /></span></span></span></span></div></span></h2><p style="text-align: left;">Back to Ben: </p><p style="text-align: left;">This blog post was written as part of the EuBIC Scientific Communications workshop by 2 great up and coming scientists!</p><p style="text-align: left;">Louise Marie Buur who is a PhD student in the Bioinformatics Research Group at University of Applied Sciences Upper Austria in Hagenberg and PROTrEIN early stage researcher. (<a href="https://at.linkedin.com/in/louise-marie-buur-ba7080129">LinkedIn here</a>) </p><p style="text-align: left;">and </p><p style="text-align: left;">Arthur Grimaud who is a also a PROTrEIN early stage research and PhD Student in Computational Proteomics at Syddansk Universitet - University of Southern Denmark. (<a href="https://dk.linkedin.com/in/arthur-grimaud">LinkedIn here</a>)</p><p style="text-align: left;">In addition to getting their PhDs in things that would make them enormously employable whenever they're done (just pop in on the Old Time Proteomics Radio Hour to hear PIs trying to steal each other's bioinformaticians) they also run <a href="https://protrein.eu/blog/">a blog for PROTrEIN (check it out here)</a>! I'm working on putting up a permanent page over there ----> somewhere that is title something like "real proteomics blogs" or "...blogs I read..." or something. </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-16017655378279341932024-02-10T03:15:00.000-08:002024-02-11T03:34:32.409-08:00Automatable cell surface proteomics (surface-omics) with magnetic beads! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjYp5vQKSs0CfZ-_ldSvusYak0wY59fPqCnh9MPdrnlEcdRiJWTiyEXmVrrbuILqyEmbkkeB69f5MNq7It9YlOM3iLw3T3ndHZv3CN4UpBZFt3Jzn5Ps6cho3pGQiy9Zw2_VmvyL6bHZkP3iyH3CsioDeVAtD-PFXmbgh4YiDX3bK8revyypuPtP-AMAoI" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="500" data-original-width="394" height="632" src="https://blogger.googleusercontent.com/img/a/AVvXsEjYp5vQKSs0CfZ-_ldSvusYak0wY59fPqCnh9MPdrnlEcdRiJWTiyEXmVrrbuILqyEmbkkeB69f5MNq7It9YlOM3iLw3T3ndHZv3CN4UpBZFt3Jzn5Ps6cho3pGQiy9Zw2_VmvyL6bHZkP3iyH3CsioDeVAtD-PFXmbgh4YiDX3bK8revyypuPtP-AMAoI=w498-h632" width="498" /></a></div><br /><p></p><p>70% of our drugs target proteins at the cell surface! Real number.</p><p>And mass spectrometry based proteomics is....sort of lousy at identifying them! There are bunches of methods out there, but what would you do if you needed to look at a lot of samples in a semi- or fully automated way? </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo5yhTjqCzuQUFzzbCweQTtlo5Sx12ZE26Jct0Jf3qPZSjAGoStPS-k-zTqFrlb-fEzN0-n1ZmuN1cyJP_G2kr9an38_kSvB14Ps93kjkKpCt2r9aDjfNx2EZ0y3aJbNRfOfCWlcUoXDMge9k9cieTojpwC4OlJtMR9u2sqvQBWWkKVLtrJMROUoKBeQ4/s2080/Screenshot%202024-02-11%20at%206.20.12%E2%80%AFAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="614" data-original-width="2080" height="167" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo5yhTjqCzuQUFzzbCweQTtlo5Sx12ZE26Jct0Jf3qPZSjAGoStPS-k-zTqFrlb-fEzN0-n1ZmuN1cyJP_G2kr9an38_kSvB14Ps93kjkKpCt2r9aDjfNx2EZ0y3aJbNRfOfCWlcUoXDMge9k9cieTojpwC4OlJtMR9u2sqvQBWWkKVLtrJMROUoKBeQ4/w569-h167/Screenshot%202024-02-11%20at%206.20.12%E2%80%AFAM.png" width="569" /></a></div>Okay...when you put the entire schematic together at the top it does look like a..lot...but when you really break it down into constituents it probably is t<a href="https://pubs.acs.org/doi/full/10.1021/acs.jproteome.3c00432">he easiest method for Cell Surface Proteomics (cell surfaceomics?) that I've seen. PLUS all these things are amenable to automation! </a><p></p><br /><p>Now, there are a lot of methods out there, with my go to being <a href="https://www.nature.com/articles/nprot.2006.359">Josip Blonder's classic work</a> on the topic but the weakness of this method and several of the others is that it enriches membranes indiscriminately (which probably still helps) but newer methods like the topic story of this post do alter the actual proteins on the outside of the cell so you are selectively enriching for those. Looking for the next drug target <i>en masse</i>? This method might be a great place to start! </p><p>Next question, of course, is "can I load t<a href="https://www.cellsurfer.net/surfacegenie">hese data into SurfaceGenie</a>?" I bet you can! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-85630749636142372442024-02-09T15:34:00.000-08:002024-02-10T16:38:23.133-08:00So....how about 1.4min plasma proteomics? <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieKQsnzepNvh8RTHYKpv-RWnfPj4QiELs8sddb1FdcwdYTEpgPz6VzgrW9y4J6GjbCqJ0Ee1wAkgutAw1ba-dNBlDPT2OzjbMQzSvgt526a1r55kYKPGJwH2V4c4ryoqmQv1FPx8lN1ZCQDBG46a7DJwGvXtq5rw_vkKPsHSVGT7hYW_DkjpsLiWYXW8g/s1410/Screenshot%202024-02-10%20at%206.34.52%E2%80%AFPM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1364" data-original-width="1410" height="460" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieKQsnzepNvh8RTHYKpv-RWnfPj4QiELs8sddb1FdcwdYTEpgPz6VzgrW9y4J6GjbCqJ0Ee1wAkgutAw1ba-dNBlDPT2OzjbMQzSvgt526a1r55kYKPGJwH2V4c4ryoqmQv1FPx8lN1ZCQDBG46a7DJwGvXtq5rw_vkKPsHSVGT7hYW_DkjpsLiWYXW8g/w475-h460/Screenshot%202024-02-10%20at%206.34.52%E2%80%AFPM.png" width="475" /></a></div><br /><p></p><p>LCMS based proteomics isn't a "high throughput" technology, right? I mean, you hear it all the time. I sure as hell hear it ALLLLLLLLLLLLL the time here in Genome Alley. "If you get the $20M transcriptomics platform and you load 1,000 library preps on it, it'll knock it out IN A DAY."</p><p>In that same amount of time....<a href="https://www.biorxiv.org/content/10.1101/2024.02.06.579213v1">you could also knock out a pretty impressive depth of 1,000 human plasma samples.</a>..</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZSq_QVI5h3IkFagFbmiSzmQHmUDf5ep8mQuDLIG_AhuGQKNEJVQxmWSBApBvhqfWev5kOCnighVd5OVTZRvOK5Ozg7xKl-ZrX_llzEV0ooKULRwhRfyoM9bYs8xrcxS7F2be8ZQpT2ldkN97pe1nKfUw2JvTMkaaMyfq2dhx5Upg675DBzsoqgmTsiq4/s1410/Screenshot%202024-02-10%20at%206.38.18%E2%80%AFPM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="1410" height="202" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZSq_QVI5h3IkFagFbmiSzmQHmUDf5ep8mQuDLIG_AhuGQKNEJVQxmWSBApBvhqfWev5kOCnighVd5OVTZRvOK5Ozg7xKl-ZrX_llzEV0ooKULRwhRfyoM9bYs8xrcxS7F2be8ZQpT2ldkN97pe1nKfUw2JvTMkaaMyfq2dhx5Upg675DBzsoqgmTsiq4/w525-h202/Screenshot%202024-02-10%20at%206.38.18%E2%80%AFPM.png" width="525" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjntHvZKMyuuAiz0CGtQhPybGMoQmSPSbirdmMPXiEQ0Ykcs16Do9eUdAtBdqbaiiB0iziPkJeECWmT5R7EHPc1QKu_4nlMrfjUowxWV1Fu-nIOwEAnGERc3O75WP2az10WvLThR5YVtakEaaDfCY7tyg8Jy9dW1G79i3kLHmkFoTI6lrMwJF0D6vaiVqY/s498/wtf-what-the-fuck.gif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="448" data-original-width="498" height="288" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjntHvZKMyuuAiz0CGtQhPybGMoQmSPSbirdmMPXiEQ0Ykcs16Do9eUdAtBdqbaiiB0iziPkJeECWmT5R7EHPc1QKu_4nlMrfjUowxWV1Fu-nIOwEAnGERc3O75WP2az10WvLThR5YVtakEaaDfCY7tyg8Jy9dW1G79i3kLHmkFoTI6lrMwJF0D6vaiVqY/s320/wtf-what-the-fuck.gif" width="320" /></a></div><br /><p>I think this guy from Annapolis is over-reacting. This isn't the first time we've seen some crazy numbers out of flow injection proteomics from this PI. He's been messing around with this stuff since he was in Wisconsin, but with ever increasing numbers.</p><p>But on plasma? With the 10-order of magnitude concentration range? This is big time. FAIMS was used here, but - FAIMS is great, but it's got a resolution of approximately 10. For that reason...use FAIMS, don't use FAIMS, it's not that big of a difference for most things, right? Running a 2.8 minute injection on this setup would give you about a resolution of 2, right? </p><p>These nanoparticles might need a serious investigation. Super cool study all around! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-4822531394103634272024-02-08T07:20:00.000-08:002024-02-09T07:24:15.880-08:00ProteoBench is coming! Register to see what the fuss is all about 2/27! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg32LiBNpuOl2H-lM9oPf3t9PE_-xo_Ykj_RjgUivsliofnRsouUXCcK_h3Zo4eYYOPy-TZZp0mRDWLN9evO4jWCwc6eLNVtd_w02kn36JlpmC3bVLJDMz4auv9_DMyexAdPIW-vApAsoBOuL3i07BL5vzStCsxPPt2153t64ncUOYR2FmmDBnbx9huL88/s921/Screenshot%202024-02-09%20at%2010.21.15%E2%80%AFAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="921" data-original-width="802" height="501" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg32LiBNpuOl2H-lM9oPf3t9PE_-xo_Ykj_RjgUivsliofnRsouUXCcK_h3Zo4eYYOPy-TZZp0mRDWLN9evO4jWCwc6eLNVtd_w02kn36JlpmC3bVLJDMz4auv9_DMyexAdPIW-vApAsoBOuL3i07BL5vzStCsxPPt2153t64ncUOYR2FmmDBnbx9huL88/w437-h501/Screenshot%202024-02-09%20at%2010.21.15%E2%80%AFAM.png" width="437" /></a></div><br /><p></p><p>Regardless of what the outside world might think we have, the proteomics community (and - to be fair -genomics isn't all there yet, either) fully complete, FAIR (which is also a thing), trackable and reproducible workflows. </p><p>It's actually a big deal to a lot of people out there.</p><p>You might have heard the word "ProteoBench" come up on THE Proteomics Show (is that still going on?) on a couple of recent episodes.</p><p><a href="https://proteobench.cubimed.rub.de/">Find out WTF it is on 2/27! It's a seriously big deal. </a></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-42630793390881757782024-02-07T08:03:00.000-08:002024-02-07T09:17:16.133-08:00Proteomic Testing Act Passed! What it means! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgDngEwsIdNGn8-9blKS0HSbhW0gA3FNO86eGFi3wXdkX37zf2XlmJf9KMU-JX4nK3K64SSJaLMkPnsHlf5MWYDo4-J1dgQtRWPReF_WxN-9h2pcJcCuYfwCN_EZk5Qn4-fUinD4ERw04wLXYeYauDbkhvBrmaaxJ1tJM6-b18JCIfU6horu6vMlmpK4_g" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="201" data-original-width="251" height="346" src="https://blogger.googleusercontent.com/img/a/AVvXsEgDngEwsIdNGn8-9blKS0HSbhW0gA3FNO86eGFi3wXdkX37zf2XlmJf9KMU-JX4nK3K64SSJaLMkPnsHlf5MWYDo4-J1dgQtRWPReF_WxN-9h2pcJcCuYfwCN_EZk5Qn4-fUinD4ERw04wLXYeYauDbkhvBrmaaxJ1tJM6-b18JCIfU6horu6vMlmpK4_g=w433-h346" width="433" /></a></div><br /><p></p><p>The biggest news for proteomics for 2024 isn't some silly expensive new instrument. It isn't dueling labs trying to see who can throw the most money at a single cell. <a href="https://www.cms.gov/medicare-coverage-database/view/article.aspx?articleid=59646&ver=2&bc=0">It is absolutely, without a doubt, this little tiny bit of legislation</a> last week. <a href="https://www.palmettogba.com/moldx">More details here</a>! </p><p>For a <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9971545/">decent analysis of what this could mean you can check out this paper from last year</a>. (It should be open access). </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjsvhRJdvCQRx4iS2SwNZjsN2Yg2_6qIMtxY5yAUF3Ke-vd91E4HS35-COvgQKfOaeoOujhKXeUH110gfAI1fsYib7wC59glN3EygNcHddVM92w9MXZaixfW4d1hV7ENsrjqbKXeFmACpG4mfRHBD82h-5eMrXDOk_id3Ncc1nTeQkYr5xq8OkWY5TrLEw" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="347" data-original-width="865" height="198" src="https://blogger.googleusercontent.com/img/a/AVvXsEjsvhRJdvCQRx4iS2SwNZjsN2Yg2_6qIMtxY5yAUF3Ke-vd91E4HS35-COvgQKfOaeoOujhKXeUH110gfAI1fsYib7wC59glN3EygNcHddVM92w9MXZaixfW4d1hV7ENsrjqbKXeFmACpG4mfRHBD82h-5eMrXDOk_id3Ncc1nTeQkYr5xq8OkWY5TrLEw=w494-h198" width="494" /></a></div>The short story is that one of the biggest hurdles in getting proteomic diagnostics out there in the world helping people has been kicked right over. There is a billing mechanism so that labs performing these tests can get paid for said tests. <p></p><p>If you're someone who filled out the recent Twitter survey on what "clinical proteomics" means last year and you selected "analyzed the proteomes of human samples" stop reading right here and go back to what you're doing. This news is not for you. This news is for the minority of people who got the answer correct. Despite the.....things.....that often manage to get published in the "journal" called "Clinical Proteomics", running HeLa dilutions is not what this is about. </p><p>Clinical proteomics is the application of protein measurement technologies to inform a clinician of information to aid in patient diagnosis. Any sort of clinical assay needs to be rock solid. From a thorough (and special) validation of the instrument that you've purchased (if not a special approval from the design of the device to qualify it for medical testing) through the strict monitoring of where that sample is in your lab - at all times - and what has been done to it, it's serious stuff. Even your scales and pipettors have to be manufactured in a compliant environment with calibrations checked and monitored routinely. Randomly people will show up by surprise and try to find you slouching. Failed that 4pm QC? Cancel plans. You're recalibrating and then you are randomly pulling samples you ran between the last QC that passed. You slipped 2 standard deviations in more than 10% of the random samples? You're re-running every. single. one. of them. That's what it's like in clinical chemistry. For real.</p><p>Whew. With that out of the way....</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_CFQDhBPTHM0reKs9eN9bR4gRVk2nBhVaGvqo84xWZq23hTQpfNdPKNj88w7oHSUeS5liOEVafS2SmhWmYIlUkK1c6SKPdE_z-eCqoGryHag7l0c5zM0QyvmSv-kMQc20vPU2E3MThsZ2xNCSjDk6S-lPraNCq53IxOYX6gJH7KDTzLCkOm54TIqhVhY/s887/im-so-excited-lucille-bluth-screaming-wbllopci9cu5xm1x.gif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="887" height="281" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_CFQDhBPTHM0reKs9eN9bR4gRVk2nBhVaGvqo84xWZq23hTQpfNdPKNj88w7oHSUeS5liOEVafS2SmhWmYIlUkK1c6SKPdE_z-eCqoGryHag7l0c5zM0QyvmSv-kMQc20vPU2E3MThsZ2xNCSjDk6S-lPraNCq53IxOYX6gJH7KDTzLCkOm54TIqhVhY/w499-h281/im-so-excited-lucille-bluth-screaming-wbllopci9cu5xm1x.gif" width="499" /></a></div><br /><p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHH!!!!!!!!!!!!!!</p><p>This is so huge for anyone with aspirations of really really doing clinical proteomics. This is the gateway to getting the attention of company's to take those biomarkers you found for early detection of disease A and condition B actually out there in the wild where they will really and truly do things. </p><p>Self-serving entry time ---> if you've got biomarkers and you need help getting that panel out there in the world, I'm willing to talk. If you're an investor hoping to capitalize on this new market, I just got my DUNS. Clearly this blog is what everyone here knows me for, but I started doing clinical chemisty 21 years ago. What a lot of business people know me for is as the sole inventor of the very first (and still possibly only) high resolution LCMS assay to operate under ISO and US DOH regulatory compliance guidelines. No joke, I took a brand new quadrupole Orbitrap and made it a fully compliant testing device. Pain. In. The. Butt. But it would be easier to do it a second, third, or twelfth time. </p><p>Either way, it's time to stop screwing around and help people! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-67644243945514005662024-02-06T14:40:00.000-08:002024-02-06T14:40:00.278-08:00Genes are not the blueprint for life. Duh.<p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjFBF1OPJWxF_Vf3AYtvWybkcyi6EdQ8BTKU5WANDPaLbtPOctE9XZBeHYRwJ5QvhYKGZJAECmU0Kr8lmm_jJXnu031niCYpaZ8bdT3btLKCottaTyDUYqPXZciLLhBIZpty3jKQpg-enz13hX71DYZJGV1XbK0oPDjKSNrjHnXCns-35bwN6PeFKXlKUc" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="817" data-original-width="858" height="465" src="https://blogger.googleusercontent.com/img/a/AVvXsEjFBF1OPJWxF_Vf3AYtvWybkcyi6EdQ8BTKU5WANDPaLbtPOctE9XZBeHYRwJ5QvhYKGZJAECmU0Kr8lmm_jJXnu031niCYpaZ8bdT3btLKCottaTyDUYqPXZciLLhBIZpty3jKQpg-enz13hX71DYZJGV1XbK0oPDjKSNrjHnXCns-35bwN6PeFKXlKUc=w488-h465" width="488" /></a></div><br /><p></p><p>While it would be fun to put in a lot of gifs here, I'm going to do just one. And it was tough to not drop 4 SpongeBobs somewhere here.</p><p><a href="https://www.nature.com/articles/d41586-024-00327-x#:~:text=When%20the%20human%20genome%20was,determined%20from%20their%20DNA%20sequence.">This is a review of a book and both the book and the reviewer</a> seem to have gotten past what 99.99% of Genome Alley has not, and started to think that maybe -just maybe - Petabytes of genomic data aren't going to fix all of medicine. </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzu2oKOkAtIlOSwri_ZEWsKY6jVix7yRc53W8XuQdLXK-4OIPoa6RvJZKa3q6FMYVU0FqKsbErafK4iA2E84YqEQoWEYrBjI0m3KU3W25mksEKLicvQPE7oae1U0t6pRbaDbx3pCZVoKPUNUvlC5QIhmiFggk6Kb959n4eTZ7GfQNgeL8GT8sJbPbNH0Y/s520/obvious.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="302" data-original-width="520" height="299" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzu2oKOkAtIlOSwri_ZEWsKY6jVix7yRc53W8XuQdLXK-4OIPoa6RvJZKa3q6FMYVU0FqKsbErafK4iA2E84YqEQoWEYrBjI0m3KU3W25mksEKLicvQPE7oae1U0t6pRbaDbx3pCZVoKPUNUvlC5QIhmiFggk6Kb959n4eTZ7GfQNgeL8GT8sJbPbNH0Y/w514-h299/obvious.gif" width="514" /></a></div><br /><p>No joke, though, this book is next up on my list. I finally started Ian Christie's magnum opus - and, yes, it is probably going to be worth it, but that dude can expound....so it might be a while....</p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-89362917000790837072024-02-05T14:21:00.000-08:002024-02-06T14:24:36.794-08:00Pulled Tip Columns are back! ESI Source Solutions! <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEg_hsHjbd6I3iwb-HxaN-QotrZ_BsWGlvwQwyG_fUMpdEyBZ1zGxsmXjkMvePcfGOpNuCy3SLkK_7GVuBsHLbRtJy7gRzyP_E-TwDrB0jwlv1hjwqHiIHVo2SRnzqIqtwRSr_M0gDUPV9llerJOc32SU3AI67KlnB_r3hnNEgkmj_m09CHfervQHcR_QHQ" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="785" data-original-width="1322" height="294" src="https://blogger.googleusercontent.com/img/a/AVvXsEg_hsHjbd6I3iwb-HxaN-QotrZ_BsWGlvwQwyG_fUMpdEyBZ1zGxsmXjkMvePcfGOpNuCy3SLkK_7GVuBsHLbRtJy7gRzyP_E-TwDrB0jwlv1hjwqHiIHVo2SRnzqIqtwRSr_M0gDUPV9llerJOc32SU3AI67KlnB_r3hnNEgkmj_m09CHfervQHcR_QHQ=w494-h294" width="494" /></a></div><br />If you're still trying to find a <a href="https://esisourcesolutions.com/shop/p/improved-pulled-tip-column-type-3-50cm-with-zircofit-sleeve-and-vici-ferrule">vendor for pulled tip custom columns, there is finally one in the US again!</a><br /><br /><p></p><p><br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-21957475794266064282024-02-04T14:22:00.000-08:002024-02-04T14:22:47.691-08:00What are those holes in the US HUPO agenda each evening? They're fun VMO functions! <p> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEi7Xel5Sp85ANv4WYwR07pJDWZRF0cs4WrhETuD1NxoBoQs-tqjArNcij6EwgdMXoM4OvLQf2ULTGFZeuimDeUln8deHf9XkaLUDgqpkHo-WFheChTWfbwfyJjDoPwu3rsnfwA8pLQMQC563ddWObPA9XSkFGXM6HeYt7Ap-1NuynHGZBrGJNyeABCQrMA" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="907" data-original-width="618" height="664" src="https://blogger.googleusercontent.com/img/a/AVvXsEi7Xel5Sp85ANv4WYwR07pJDWZRF0cs4WrhETuD1NxoBoQs-tqjArNcij6EwgdMXoM4OvLQf2ULTGFZeuimDeUln8deHf9XkaLUDgqpkHo-WFheChTWfbwfyJjDoPwu3rsnfwA8pLQMQC563ddWObPA9XSkFGXM6HeYt7Ap-1NuynHGZBrGJNyeABCQrMA=w454-h664" width="454" /></a></div><br /><p></p><p>The US Human Proteomics Organization's 20th anniversary is coming up <a href="https://www.ushupoconference.org/agenda">so fast that the Agenda is now up!</a> </p><p>Dr. Neely said this better...so...</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgd6rGKj9Xpc2WPcpajNOuWlfKqJKv6RkwP4_AToFp0p-6Njz-tNWUpvP_JbS2U4gY2IMhd6262vwVB_wx1eAcGXvchzhGec_-4SJToEJDUfBakpZ4lvl3ci37U8p3AKVZKctqN_l8zWKoXt7sAZ2Tp2F2lsV3AJ33JzwOrbfQoA7eYGGf3LbtHOOA1jBc" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="569" data-original-width="530" height="493" src="https://blogger.googleusercontent.com/img/a/AVvXsEgd6rGKj9Xpc2WPcpajNOuWlfKqJKv6RkwP4_AToFp0p-6Njz-tNWUpvP_JbS2U4gY2IMhd6262vwVB_wx1eAcGXvchzhGec_-4SJToEJDUfBakpZ4lvl3ci37U8p3AKVZKctqN_l8zWKoXt7sAZ2Tp2F2lsV3AJ33JzwOrbfQoA7eYGGf3LbtHOOA1jBc=w460-h493" width="460" /></a></div><br />...we did a play by play of this year's agenda! <p></p><p>What we didn't cover were the 2 evening holes in the Agenda that didn't say anything. As the chair of the VMO I felt like I should know which night was what, as they are our activities. HOWEVER.</p><p>Monday night is going through the winning entries of the VMO Proteomics Video Competition! We extended the deadline until 2/15 for late breaking entries. Come on, you clever young tik tokers, and short YouTubers we know you've got something up your sleeves. Reminder, there is prize money.</p><p>Tuesday night's unlisted slot is the (requested by the leadership, for the record, I think it's a poor idea) live recording of THE Proteomics Show. It worked in Germany. I'm skeptical about reproducing it as well somewhere that I don't know the language, but US HUPO funds the program, so we're gonna do it anyway! </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-3693238014525650573.post-65131996901203065322024-02-03T02:34:00.000-08:002024-02-03T02:37:06.222-08:00Single Cell Proteomics made Gen News! <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSO1RkHc0Z36HH7o48ELIygY6BwsyuiWKlfQmpeI-qdW3V4DEBEKXVQLm4LvLnUudlx1B3-cvE9jcCUYVNFMoF7nhru-7wmQzJGegmBZQqeZIfeSUfjduv5LNg0v0F3pllt5FKK946enWheN4x6kdgGglvuqVffApM0DB0KC1r52E0YIWukhhu7vyVAGo/s2162/Screenshot%202024-02-03%20at%205.35.58%E2%80%AFAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1916" data-original-width="2162" height="485" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSO1RkHc0Z36HH7o48ELIygY6BwsyuiWKlfQmpeI-qdW3V4DEBEKXVQLm4LvLnUudlx1B3-cvE9jcCUYVNFMoF7nhru-7wmQzJGegmBZQqeZIfeSUfjduv5LNg0v0F3pllt5FKK946enWheN4x6kdgGglvuqVffApM0DB0KC1r52E0YIWukhhu7vyVAGo/w548-h485/Screenshot%202024-02-03%20at%205.35.58%E2%80%AFAM.png" width="548" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div><br />I know proteomics people are probably tired of hearing about single cell proteomics from every angle, but the rest of the world can't seem to get enough of it! <p></p><p>More proof? Check <a href="https://www.genengnews.com/topics/omics/mass-spec-based-single-cell-proteomics-grapples-with-heterogeneity/">out this brand new article in Genetic Engineering News</a>! </p><p>It's a surprisingly well-balanced analysis of where we are from a technology stand point. Of course, the absurd numbers Karl's group has been showing off makes the article, and you can't write an article on SCP without Slavov lab. Our field's favorite picoliter robotics systems are highlighted as well as my group's early results on the ZenoTOF and TIMSTOF Flex! Perhaps the 7am seminar isn't the best place to get a sound bite from me about the difficulties in making nanoflow chromatography accessible to non-mass spec nerds, but sometimes you need some emotion in your words? </p>Unknownnoreply@blogger.com0