Christopher Rose

For those looking for a new proteomics opportunity, there is a position open within the Translational Medicine group. This is a fantastic opportunity to perform impactful research using cutting edge technology. Check it out below! careers.gene.com/us/en/job/2024…

@drmcaswell @ucl Congratulations! Maybe next time I am in the UK I can stop by for a lab visit!

@ProteomicsNews I found one of these papers…and I couldn’t find the methods section. Maybe I missed it or I have a misconception of what preprints are/should be. I had thought they were the submitted versions of papers in their entirety…that would include data availability too.

@ProteomicsNews Sorry you couldn’t make it. Appears I will be standing in for you during the panel discussion. Too bad because I was looking forward to seeing if you had any spicy takes. Maybe next time!

@mjmaccoss @DemichevLab @seer_bio The current v1.9.1 license was also a non-starter for us, which is too bad. Hopefully will change going forward but we are already investing in alternative options.

DIA-NN in the cloud workflow by @seer_bio biorxiv.org/content/10.110…

@nesvilab @HippHupo I saw the agenda and was jealous of those that were able to attend! Such a great collection is speakers mixed in with tutorials is the recipe for a great time.

How is it no one yet twitted how amazing was the @HippHupo immunopeptidomics summer school this week in Montreal? Well organized, great talks and posters, engaged audience. I was fortunate they invited me to talk about our work and do #FragPipe tutorial. hupo.org/Human-Immuno-P….

@chrashwood Maybe its hard since we are in industry. Lots of paperwork. At least that is what I tell myself. 🤷‍♂️ We used to get things a bit early, but only when the launch was imminent. These tags will take some getting used to so hopefully we can get them soon to start figuring things out

@chrashwood I heard it will be available later this year, but no official time. Disappointing given they “launched” it at ASMS. We arent VIP so haven’t gotten our hands on it yet. Coaleswnce will be on our minds as we optimize methods. And yeah with that high mass error looks like coalesence

@chrashwood Me watching this thread play out…

@ProteomicsNews First thing I did when I bought a new chair for my house. Way better experience and easier on the floors.

Very excited to see work from Hanna Budayeva included in this special issue of @JProteomeRes. Hanna has done a fantastic job leading our chemoproteomics efforts over the last few years - this story is just one of the exciting things her group is working on! Check out this issue!

@chrashwood @ItsBiniR @ProteomicsNews @Smith_Chem_Wisc Microscans could help to improve signal while avoiding potential coalescence, just not sure it would be worth it. Injecting 2x ions can improve signal to noise by 2x, 2 microscans only improves signal to noise by sqrt(2).

While the proteomics world is getting excited over a 35plex possibility, the metabolomics world is casually dropping 96plex workflows.. 🤯

@ItsBiniR @ProteomicsNews @Smith_Chem_Wisc NuCode…a decade ago…ouch. Time comes at you fast. Funny enough working on NeuCode is where I got lots of experience measuring coalescence with 3 mDa and 6 mDa mass differences. Seems like that experience might start coming into relevance again.

@ProteomicsNews @Smith_Chem_Wisc Yeah.. Totally forgot about the NeuCode SILAC thingy from a decade back or so.. Didn't realize it was available as 16plex.. Or is this a different strategy?? Need to look for the paper now..

@ProteomicsNews @AmandaLSmythers @chrashwood @ItsBiniR You are correct. I saw those peaks and thought Astral b/c I assumed no one would set the Orbitrap at a resolution that doesn’t baseline separate TMT. But yeah, with updates to TurboTMT Orbitrap analysis will be Ok. Still worried about coalescence popping up more often for folks.

I have officially come to that age where the first response to new tech is uttering wtf.. Its gonna take a while to be fine with that baseline.. TMT35plex ions from 4 adjacent channels.. 🤓 Many thanks to the authors for sharing the raw files on MassIVE.. massive.ucsd.edu/ProteoSAFe/dat…

@ItsBiniR @chrashwood If you do increase AGC or max IT you also need to be careful of space charging and coalescence. Coalescence will happen sooner at 3 mDa than it does at 6 mDa so it might start to become too much of an issue if you have too high of signal within neighboring channels…

@CMichaelRose @chrashwood I am very curious on how much sample concentration can be loaded per channel for these 35plex as well.. 1/35th of sample representation in each spectra would require more starting material and fractions?? 🤔

@ItsBiniR @chrashwood Real issue is increased multiplexing splits the ions into more channels. For equal number of precursors each channel has half the number of ions (16 to 32 plex). You don’t need more starting sample, you need to increase AGC and potentially max injection times. Sounds familiar…

@AmandaLSmythers @chrashwood @ItsBiniR I agree…but I assume this will become standard practice 😔. No one looks at spectra anymore. Hopefully Thermo will fix it, it certainly will bother me.

@chrashwood @ItsBiniR I hope this wasn’t used quantitatively…

@ItsBiniR @chrashwood 50K is needed to resolve 6 mDa, and was added for 10 plex reagents and can be used for 16/18 plex. For a 3 mDa difference you will need more resolution. There are also a ton of space charging considerations with 3 mDa, would be interesting to look at but I have other things to do

@chrashwood Oops.. 😉 Eventhough 50k resolving power is what theoretically needed to separate those 3 mDa delta mass, it has always been a practise to resolve 6 mDa TMT18plex at 120k resolution to ensure baseline resolution.. TMT-MS3 at 120k resolution should be good for 35plex..

Great work out of @susanklaeger’s lab. Denys was a fantastic intern. He not only spearheaded this project, but also helped with optimization of DIA methods for our timsTOF. Thanks @fmeierX for being supportive of his time with us! Check out the paper, some great findings there!

@byu_sam These data are in the hands of many within the ML community already. This is probably the most impactful use of machine learning on mass spec data within Pharma at the moment. If you’re looking for specific papers here’s one but there are many many others ncbi.nlm.nih.gov/pmc/articles/P…

@CMichaelRose I’m trying to get that data into the hands and machine learning community. This project is a clearing house that brings together machine learning people with scientific people. The machine learning people need well-defined tasks and data sets that they can use to build models.

Hey #TeamMassSpec. this resource includes peptide/MHC prediction tasks - but it looks like they don't have much mass spec data. Can we fix that? I know there are people with hard data (not predictions) of peptide binding to MHC. #ProteomicsFTW