tag:blogger.com,1999:blog-3693238014525650573.comments2024-03-19T00:20:07.007-07:00News in Proteomics ResearchUnknownnoreply@blogger.comBlogger1146125tag:blogger.com,1999:blog-3693238014525650573.post-45633625745167777642023-12-14T11:11:59.468-08:002023-12-14T11:11:59.468-08:00Huh? Do you mean cmd+shift+5 which has been in Mac...Huh? Do you mean cmd+shift+5 which has been in MacOS since forever ;-)Lukenoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-71945049579834795292023-12-14T06:06:22.081-08:002023-12-14T06:06:22.081-08:00My PhD Prof back in India has an LTQ Orbi VelosPro...My PhD Prof back in India has an LTQ Orbi VelosPro with nLC1000 running smooth for over a decade..Bini Ramachandrannoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-24154580587173663022023-12-11T14:55:44.471-08:002023-12-11T14:55:44.471-08:00Hydroxyproline is mostly incorporated as an AA int...Hydroxyproline is mostly incorporated as an AA into collagen. There’s **tons** of it.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-62499870500583441602023-12-11T09:24:47.059-08:002023-12-11T09:24:47.059-08:00Hi Ben, interesting data. I think the loss of hydr...Hi Ben, interesting data. I think the loss of hydrophilic peptides should not be that dramatic ~0.7 % ACN reduction in hydrophobicity is ~the same 0.7-0.8% in the number of detectable peptides. It would be nice to compare hydrophobicity of your detected peptides at both FA and AA and see, which population is missing. Another question here is the consistency of your LC / eluent system: the major peak on chromatogram shifted right under AA conditions, plus all peaks appeared to be significantly wider...this is very unlikely with the system working properly - retention should be lower.<br />Thanks! OlegOleg Krokhinnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-65319963958199849352023-12-10T10:47:30.326-08:002023-12-10T10:47:30.326-08:00Ridiculous review . Did not know Targetted proteom...Ridiculous review . Did not know Targetted proteomics is expensive Bharath Kumar Raghuramannoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-61528729894716247092023-12-04T06:07:43.760-08:002023-12-04T06:07:43.760-08:00From S44: "The MS1 scan range covered with DI...From S44: "The MS1 scan range covered with DIA windows was set from 400 to 1000 m (about twice the height of the Empire State Building)/z (inclusion list covering 40 DIA windows starting at 407.5 ..." Is mention of the Empire State building there some sort of DIA-specific terminology, or do we owe the authors a great deal of thanks for what looks like an incredibly random insertion of metric trivia into the supp. method section?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-1260060405747683672023-11-17T11:27:55.429-08:002023-11-17T11:27:55.429-08:00Venny is great, but if you want proportional Venn ...Venny is great, but if you want proportional Venn diagrams give this one a try https://www.deepvenn.comLabenskinoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-84724256882682536362023-11-08T04:14:06.265-08:002023-11-08T04:14:06.265-08:00I appreciate you making the effort so I don't ...I appreciate you making the effort so I don't have to :DSarumitehttps://www.blogger.com/profile/17920058089024577672noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-5406267906681858582023-11-05T20:59:49.503-08:002023-11-05T20:59:49.503-08:00The dataset is huge and is not downloadable by neo...The dataset is huge and is not downloadable by neo4j communtity users. It could be split and made available as separate csv files. (I need only medicinal and indications data). CKG seems to be vast and a commendable work!!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-87383226971568793082023-10-30T16:21:30.578-07:002023-10-30T16:21:30.578-07:00LNI Swissgas also makes a N2 generators, and one o...LNI Swissgas also makes a N2 generators, and one of the options will supply both the ESI source purity AND the collision cell purity N2! Works great!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-29255807535579233672023-10-30T08:06:41.143-07:002023-10-30T08:06:41.143-07:00Hey ben, you can may be give a trial here : https:...Hey ben, you can may be give a trial here : https://www.biotools.fr/misc/vennyAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-49243022371077761352023-10-23T13:01:17.880-07:002023-10-23T13:01:17.880-07:00Give https://fuzzylife.shinyapps.io/venn/ a try 🤓...Give https://fuzzylife.shinyapps.io/venn/ a try 🤓Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-75334645062904765252023-10-23T05:58:25.146-07:002023-10-23T05:58:25.146-07:00Have you tried... https://www.biotools.fr/misc/ven...Have you tried... https://www.biotools.fr/misc/vennyJ Neilnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-75006057955120378972023-10-23T00:02:45.213-07:002023-10-23T00:02:45.213-07:00Alternatively, https://jvenn.toulouse.inrae.fr/app...Alternatively, https://jvenn.toulouse.inrae.fr/app/index.htmlAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-28428914582024946342023-10-17T07:35:23.044-07:002023-10-17T07:35:23.044-07:00Will this be recorded?Will this be recorded?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-38918698101427765002023-10-04T15:53:22.483-07:002023-10-04T15:53:22.483-07:00Well, been studying statistics for a while when te...Well, been studying statistics for a while when teacher was teaching mgf, excited to see this is finally related with mass spect, but it turned out to be moment generating fuction!ssybbcnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-38944889017772472942023-09-16T12:53:43.472-07:002023-09-16T12:53:43.472-07:00I made a comment a few years ago but it never got ...I made a comment a few years ago but it never got posted. 🤞Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-59348723991535489512023-09-16T01:43:05.277-07:002023-09-16T01:43:05.277-07:00Here is the link of CURTAIN Preprint:https://www.b...Here is the link of CURTAIN Preprint:https://www.biorxiv.org/content/10.1101/2023.07.25.550405v1Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-38215187069741409512023-09-11T09:11:00.430-07:002023-09-11T09:11:00.430-07:00Hi Ben, thanks for posting about HowDirty!
The f...Hi Ben, thanks for posting about HowDirty! <br />The final manuscript was recently published, with only minor changes.<br />https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10.1002/pmic.202300134Davidhttps://github.com/DavidGZ1/HowDirtynoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-28452630412347688842023-09-11T05:21:19.781-07:002023-09-11T05:21:19.781-07:00Very interesting on the subset library approach. T...Very interesting on the subset library approach. They effectively do targeted proteomics on a longer list. To maximize that I think encyclopedia is actually a better algorithm where you get a full grid array output. All that said, I’m a bit weary of FDR here. If the target feature space is incongruent with the discovery space, I am not convinced that diann is the best algorithm. For the same reason, cancer plasma sets should probably have some of the host cancer leak proteins included in library but also to prevent false positives forced on the unmatchable signals. Maybe the complexity match changes since this is serum and not plasma, but Astral is achieving over 6000 protein ids with diann on Seer enrichment platform (bias here, I work for Seer). Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-90771313883820014602023-09-03T18:38:44.788-07:002023-09-03T18:38:44.788-07:00Gotta say that unleash the analysis is the best bu...Gotta say that unleash the analysis is the best button text i have ever seen Joel R Steelehttps://www.blogger.com/profile/04101740297152079257noreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-73347152059753622262023-08-21T06:35:48.803-07:002023-08-21T06:35:48.803-07:00But it's already out of date- missing the HP D...But it's already out of date- missing the HP D100 paper by Ryan Kelly's group!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-11354732754820783222023-07-30T18:24:04.408-07:002023-07-30T18:24:04.408-07:00Hi Ben! This is a bit of a long shot but do you st...Hi Ben! This is a bit of a long shot but do you still have the zip file for ShettiMotif? It's pretty much perfect for my project but the download link is broken and I can't get in contact with Haitham Sobhy. <br />Thank you so much!<br />JenniferAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-35183654571100534962023-07-05T07:17:08.658-07:002023-07-05T07:17:08.658-07:00I think you are showing an old version of the GUI ...I think you are showing an old version of the GUI :) In v1.8.2 beta 22, you'll see direct (legacy), Composite (high precision) and Composite (high accuracy) which is what is referred to in the preprint. <br /><br />For the gui you show, robust vs any lc specifies whether you consistently select 4 points only for integration (default true), and high accuracy vs high precision is whether (or not) you remove interfering signal in quant. <br /><br />If Vadim reads this, I'd hope he can re-integrate the various options in the gui cap Ben shared. I'd be more okay with 6 options than 3 with one of the options being somewhat ambiguous (not straightforward to remove the --no-ifs-removal and --peak-center flags if by default setting to robust LC, high precision). Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3693238014525650573.post-87339287798511161452023-06-15T01:23:01.356-07:002023-06-15T01:23:01.356-07:00Thanks for a brief overview, Ben. Nice that someon...Thanks for a brief overview, Ben. Nice that someone still considers oxoniums to be friends. How's the annotation quality, have you maybe checked?Leriiahttps://www.blogger.com/profile/17576507890556592359noreply@blogger.com