Academic scientist at the University of Washington with an interest in #massspectrometry and #proteomics.
While I personally stopped tweeting in May, it was clear that now was the time for Flipboard to stop tweeting as well.
This is a sad outcome given that Twitter was the platform we got started on in 2010 and I was a board member there with Jack, Ev and Dick. But that Twitter is gone now. And the future is the open social web.
@RonBeavis Yasset had this idea that people can suggest such annotations via his repository and they would be taken back to PX. I don't know whether it still works but that would solve the problem?
https://github.com/bigbio/proteomics-sample-metadata
"The German government has launched a new Open Source software project called openDesk, which aims to reduce the country’s dependency on proprietary software vendors and support transparency and interoperability.
openDesk is a collection of #OpenSource software modules that are important for day-to-day work in the public sector, such as text creation, file collaboration, project management, email, calendar and messaging."
#FOSS #government #overheid #DigitalSovereignty
https://opensource.net/governments-adopt-open-source-sovereignty/
@proteomicsnews blog post | Hate your nanospray source? 3D print a better one! https://proteomicsnews.blogspot.com/2023/09/hate-your-nanospray-source-3d-print.html
---
#proteomics #prot-other
RT (X) | https://twitter.com/NatureBiotech/status/1705175781909872964
#proteomics #prot-RT #prot-paper
AITA, academic publishing edition.
Journal sends a review back to me because as reviewer I did not run the code and replicate the results.
My reply: "As an unpaid anonymous peer reviewer who handles probably 30 manuscripts a year, I am absolutely not in the position of running and evaluating code any more than I am in the position of running gels to evaluate lab results. If this is important to you, I suspect you can find a consultant who will do it at a reasonable rate."
Am I the asshole?
Almost ready for #HUPO2023 after a long trip to Busan.
I'm looking forward to chair the #ComputationalProteomics/#Bioinformatics pre-conference training session tomorrow morning (Sunday Sept 17, 9:00–12:00), together with an all-star team. Meet us there!
https://2023.hupo.org/scientific-program-program-at-a-glance/
Flew from Seattle to Frankfurt last night and was lucky enough to have a port-side window seat!
@RonBeavis I do have to say growing up in the Suburbs of Detroit that this correlation was real ;)
I do not understand why measuring the concentration of an mRNA was ever considered to be a surrogate for its corresponding protein's concentration. It is like trying to measure the number of Ford trucks in a city by determining the number of Ford factories it contains.
I see a lot of people sharing blanket condemnations of all of those who still remain on #Twitter / #Xitter , and I need you to slow down a bit.
Sure, in some cases this is justified - journalists should really know better. But there are a lot of communities on that platform that are vital to many people's well-being that _haven't_ been replicated on the #Fediverse or elsewhere. Take #BlackTwitter - while #BlackMastodon is growing, it's still minuscule in comparison. The number of Twitter users in #Pakistan is staggering, while they are only a handful on #Mastodon . And so on, and so forth. Twitter was a lifeline to many marginalized people, and it still is - even though it gets worse every day - and we need to recognize this.
As a white European guy, it was easy for me to walk away from Twitter (I still have an account there, but I only post "you should go to Mastodon" stuff these days) - since it is easy to find people of a similar background to interact with. But this is NOT true for everyone!
So I'd like everyone to show a bit less contempt to the remaining Twitter users in general, and put some more effort in how to make the Fediverse friendlier to marginalized voices. Because there is MUCH work to be done here!
Easy for you to say.
I study online disinformation.
Via the Twitter files, Musk has created an enormous amount of trouble for our research center, in addition to cutting off all access to Twitter data.
https://www.washingtonpost.com/technology/2023/06/06/disinformation-researchers-congress-jim-jordan/
@pwilmart @Chrashwood @pastelbio It is great seeing the value of RT in new AI based scoring. As someone who still does a lot of targeted proteomics it is what we have relied on for decades. The value of knowing the RT... either empirically or from good predictions is probably more valuable than knowing the accurate precursor mz. However more tools support one over the other.
@pwilmart @Chrashwood @pastelbio I agree with @Chrashwood. Who has spent a lot of time optimizing search engines (specially on DIA or PRM data) for unit resolution recently? I totally believe that search engines benefit from accurate m/z and the ability to predict RT. However we know that ion traps using calibration curves are easily 2x more sensitive than OTs.
@neely @Chrashwood It is partially counting noise and also chemical interference. Newer instruments that can use narrower precursor isolation windows and higher resolving power will minimize the interference. They are also more efficient at counting ions by making better use of the ion beam and improving the shot noise.
@neely Mike posted the graphic of the normal distributions. The top end is a tail that is captured well. The lower intensity is where you see the under-sampling of the less abundant proteins.
Maybe data on new instruments completely overlaps with the benchmark data set, maybe there’s a similar plot for plasma?
@pastelbio I looked through their proteomic findings from Vlad's letters, and I can only feel sad. I am reminded of the T. rex outcome. If the first protein in the table is Titin, what conclusion should we draw?
Any good references or repos describing best practices for normalizing relative PTM abundances to protein abundances in the same samples?
Thousands of scientists are cutting back on Twitter, many citing Musk's policies. The most popular alternative for new social media accounts is Mastodon.
https://www.nature.com/articles/d41586-023-02554-0
#mastodon #twitter #elonmusk
