Phil W
@pwilmarth.bsky.social
Old person forgetting everything they ever knew about proteomics at speeds in excess of 270 Hz...
Chip and I want to remind everyone to put your feet up, recharge the batteries, and sleep through black Friday.
November 26, 2025 at 10:29 PM
Chip and I want to remind everyone to put your feet up, recharge the batteries, and sleep through black Friday.
I see modified peptides. All of the time. They are everywhere.
proteomicsnews.blogspot.com/2025/11/pros...
proteomicsnews.blogspot.com/2025/11/pros...
a young boy laying in bed with the words " i see dead people " above his head
Alt: a young boy laying in bed with the words " i see dead people " above his head
media.tenor.com
November 26, 2025 at 2:13 PM
I see modified peptides. All of the time. They are everywhere.
proteomicsnews.blogspot.com/2025/11/pros...
proteomicsnews.blogspot.com/2025/11/pros...
Reposted by Phil W
I am looking for a PostDoc to join my group at Genentech to drive the development of proteomics technologies to fuel target and therapeutic discovery and development. Check out the link below!
careers.gene.com/us/en/job/20...
careers.gene.com/us/en/job/20...
November 25, 2025 at 12:39 AM
I am looking for a PostDoc to join my group at Genentech to drive the development of proteomics technologies to fuel target and therapeutic discovery and development. Check out the link below!
careers.gene.com/us/en/job/20...
careers.gene.com/us/en/job/20...
Are you curious about what steps you need to do to analyze very large multi-plex TMT datasets? This is a reanalysis of some Gygi Lab mouse liver data from 2015 and 2021 with 14.5 million MS2/MS3 scans in total. The big data needed a big discussion (kind of a long read).
github.com/pwilmart/mou...
github.com/pwilmart/mou...
GitHub - pwilmart/mouse_liver_TMT_reanalysis: Reanalysis of large-scale TMT mouse liver studies (2015 and 2021) from the Gygi Lab.
Reanalysis of large-scale TMT mouse liver studies (2015 and 2021) from the Gygi Lab. - pwilmart/mouse_liver_TMT_reanalysis
github.com
November 23, 2025 at 6:06 PM
Are you curious about what steps you need to do to analyze very large multi-plex TMT datasets? This is a reanalysis of some Gygi Lab mouse liver data from 2015 and 2021 with 14.5 million MS2/MS3 scans in total. The big data needed a big discussion (kind of a long read).
github.com/pwilmart/mou...
github.com/pwilmart/mou...
Reposted by Phil W
We’ve been considering creating an announcement mailing list for #PRIDE @pride-ebi.bsky.social; to share new features, releases, datasets, known issues, and more.
If you think this would be useful, please Like and RT!
If you think this would be useful, please Like and RT!
November 22, 2025 at 11:21 AM
We’ve been considering creating an announcement mailing list for #PRIDE @pride-ebi.bsky.social; to share new features, releases, datasets, known issues, and more.
If you think this would be useful, please Like and RT!
If you think this would be useful, please Like and RT!
Lucinda Brand just made 50 elite women's cyclocross podiums (placing 1, 2, or 3) in a row. That is like submitting your last 50 manuscripts to Nature, Science, or Cell and all getting accepted with no or minor revisions. It is an epic accomplishment by one of the true legends of the sport. Chapeau!
November 16, 2025 at 5:35 PM
Lucinda Brand just made 50 elite women's cyclocross podiums (placing 1, 2, or 3) in a row. That is like submitting your last 50 manuscripts to Nature, Science, or Cell and all getting accepted with no or minor revisions. It is an epic accomplishment by one of the true legends of the sport. Chapeau!
I grew up during the cold war where we had fascist "tools" using science and scientists to make weapons. Now we have scientists using fascist tools and weapons (ML and AI) in some failing effort to do good. If AI worked, it could do its own white washing. This is some real next generation absurdity.
November 12, 2025 at 12:04 AM
I grew up during the cold war where we had fascist "tools" using science and scientists to make weapons. Now we have scientists using fascist tools and weapons (ML and AI) in some failing effort to do good. If AI worked, it could do its own white washing. This is some real next generation absurdity.
In the early days, artificial limbs were made out of wood. Since it is still the early days of artificial intelligence, I am going to substitute "wooden head" for "AI" every time I see it in scientific paper titles, in conference talks, and social media posts. It puts the work in a proper context...
November 8, 2025 at 9:58 PM
In the early days, artificial limbs were made out of wood. Since it is still the early days of artificial intelligence, I am going to substitute "wooden head" for "AI" every time I see it in scientific paper titles, in conference talks, and social media posts. It puts the work in a proper context...
Joe is a great scientist and a wonderful collaborator. If you want to know more about platelets, this would be a good starting point.
October 31, 2025 at 2:54 PM
Joe is a great scientist and a wonderful collaborator. If you want to know more about platelets, this would be a good starting point.
Reposted by Phil W
To be honest, when I see conferences announced that have a majority of male invited speakers, I think the organisers are not trying hard enough. We have so many excellent #FemalesinMS and resources available there is really no excuse for it anymore #massspec #teammassspec #lipidomics #metabolomics
October 27, 2025 at 10:45 PM
To be honest, when I see conferences announced that have a majority of male invited speakers, I think the organisers are not trying hard enough. We have so many excellent #FemalesinMS and resources available there is really no excuse for it anymore #massspec #teammassspec #lipidomics #metabolomics
Some new content at GitHub:
github.com/pwilmart/pow...
We have been measuring proteomes for a long time but almost never think about our data and results at the whole proteome level. We lose a lot of information when we think one protein at a time. We need to multiplex our thinking.
github.com/pwilmart/pow...
We have been measuring proteomes for a long time but almost never think about our data and results at the whole proteome level. We lose a lot of information when we think one protein at a time. We need to multiplex our thinking.
October 27, 2025 at 11:30 PM
Some new content at GitHub:
github.com/pwilmart/pow...
We have been measuring proteomes for a long time but almost never think about our data and results at the whole proteome level. We lose a lot of information when we think one protein at a time. We need to multiplex our thinking.
github.com/pwilmart/pow...
We have been measuring proteomes for a long time but almost never think about our data and results at the whole proteome level. We lose a lot of information when we think one protein at a time. We need to multiplex our thinking.
Thermo announces partnership with big coal to develop new line of coal-powered liquid chromatography and Mass spectrometry solutions (pollutions?). It's even easier for senior PIs to "get their hands dirty" in the lab. Pull down Hibachi facilitates spur-of-the-moment lab BBQs and team building...
Anyone looking forward to purchasing an LC-MS co-developed by OpenAI?
October 17, 2025 at 7:17 PM
Thermo announces partnership with big coal to develop new line of coal-powered liquid chromatography and Mass spectrometry solutions (pollutions?). It's even easier for senior PIs to "get their hands dirty" in the lab. Pull down Hibachi facilitates spur-of-the-moment lab BBQs and team building...
This week's top headline from the Department of Redundancy Department: MTG says that there are a lot of weak Republican men...
October 14, 2025 at 7:31 PM
This week's top headline from the Department of Redundancy Department: MTG says that there are a lot of weak Republican men...
They may be a few anti-Pho folks here in Portland but they would be hard to find on a cool rainy day. As some French lady said many, many years ago, "let them eat soup!"
October 11, 2025 at 10:37 PM
They may be a few anti-Pho folks here in Portland but they would be hard to find on a cool rainy day. As some French lady said many, many years ago, "let them eat soup!"
US HUPO short course topic suggestions:
You are doing it wrong because no one knows how to do it correctly.
Techniques that actually work (*extremely* short course).
AI is to science like creationism is to evolution.
Experimental designs that tell you something: finding needles in haystacks.
You are doing it wrong because no one knows how to do it correctly.
Techniques that actually work (*extremely* short course).
AI is to science like creationism is to evolution.
Experimental designs that tell you something: finding needles in haystacks.
October 9, 2025 at 5:09 PM
US HUPO short course topic suggestions:
You are doing it wrong because no one knows how to do it correctly.
Techniques that actually work (*extremely* short course).
AI is to science like creationism is to evolution.
Experimental designs that tell you something: finding needles in haystacks.
You are doing it wrong because no one knows how to do it correctly.
Techniques that actually work (*extremely* short course).
AI is to science like creationism is to evolution.
Experimental designs that tell you something: finding needles in haystacks.
ChatStat or StatChat??? I bet this protein is always differentially something or another: www.uniprot.org/uniprotkb/Q5...
October 6, 2025 at 11:33 PM
ChatStat or StatChat??? I bet this protein is always differentially something or another: www.uniprot.org/uniprotkb/Q5...
I gave a quick listen to Taylor Swift's new album. My first thought was that I hope they are not making a video for Wood...
October 5, 2025 at 10:10 PM
I gave a quick listen to Taylor Swift's new album. My first thought was that I hope they are not making a video for Wood...
Maybe the Government shutdown means the Federal Government won't be able to terrorize "we the people" of the US as much, or are those the "essential functions" now?
October 1, 2025 at 2:14 PM
Maybe the Government shutdown means the Federal Government won't be able to terrorize "we the people" of the US as much, or are those the "essential functions" now?
Boy, I'm sure glad federal troops are coming to get crime under control here in Portland. On my walk today, I saw some cars not come to complete stops at stop signs. There were a few cars exceeding the speed limit. There were some pedestrians that jay walked. I saw some litter. It is out of control!
September 27, 2025 at 7:45 PM
Boy, I'm sure glad federal troops are coming to get crime under control here in Portland. On my walk today, I saw some cars not come to complete stops at stop signs. There were a few cars exceeding the speed limit. There were some pedestrians that jay walked. I saw some litter. It is out of control!
Reposted by Phil W
and btw, here is a much better write-up by @pwilmarth.bsky.social from 2021. pwilmart.github.io/blog/2021/04...
I just did my own internal write-up and leaned on this completely.
I just did my own internal write-up and leaned on this completely.
Go big or go home?
pwilmart.github.io
September 12, 2025 at 5:48 PM
and btw, here is a much better write-up by @pwilmarth.bsky.social from 2021. pwilmart.github.io/blog/2021/04...
I just did my own internal write-up and leaned on this completely.
I just did my own internal write-up and leaned on this completely.
I'm amazed at academics using AI. You are whitewashing the AI field for tech bros and they have rewarded your efforts with funding cuts, job losses, and incredible stress. But go ahead and keep writing those AI papers and having AI conferences. Maybe you'll raise your h-index before you're erased.
September 10, 2025 at 4:07 PM
I'm amazed at academics using AI. You are whitewashing the AI field for tech bros and they have rewarded your efforts with funding cuts, job losses, and incredible stress. But go ahead and keep writing those AI papers and having AI conferences. Maybe you'll raise your h-index before you're erased.
Size matters. How big is your embedding? Maybe we should call AI what it really is: Alpha-male Insecurity. If your research work involves AI, just stop. It is like saying you found a couple of non-mass-murder uses for assault rifles, so you recommend all researchers start using them.
September 3, 2025 at 12:44 AM
Size matters. How big is your embedding? Maybe we should call AI what it really is: Alpha-male Insecurity. If your research work involves AI, just stop. It is like saying you found a couple of non-mass-murder uses for assault rifles, so you recommend all researchers start using them.
ECD is back! That took about 20 years. Proteomics must be slowing down. The length for proteomic idea recycling is more like 10 years. Maybe ECD results in longer time distributions? Since it is shooting electrons at big things, I hope it uses a manual joystick. Turn MS into a mass player e-game!
Electron Capture Dissociation for Discovery Top-Down Proteomics of Peptides and Small Proteins on Chromatographic Time Scales pubs.acs.org/doi/10....
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#proteomics #prot-paper
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#proteomics #prot-paper
August 30, 2025 at 12:26 AM
ECD is back! That took about 20 years. Proteomics must be slowing down. The length for proteomic idea recycling is more like 10 years. Maybe ECD results in longer time distributions? Since it is shooting electrons at big things, I hope it uses a manual joystick. Turn MS into a mass player e-game!
I can confidently predict that "inflammation" and "immune response" will be associated with many diseases...
News in Proteomics Research blog post | SomaModules - Pathway Analysis for Scan Output! (And publicly available SomaScan data!) proteomicsnews.blogs...
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#proteomics #prot-other
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#proteomics #prot-other
August 29, 2025 at 3:21 PM
I can confidently predict that "inflammation" and "immune response" will be associated with many diseases...
When you are mostly concerned about the size of your study, can we all agree to call that a search for bromarkers?
August 28, 2025 at 1:23 AM
When you are mostly concerned about the size of your study, can we all agree to call that a search for bromarkers?