Christopher Rose

Senior Director of Proteomics & Group Leader @Genentech. Passion for developing proteomics technologies that fuel therapeutic discovery. Tweets are mine.

[Christopher Rose @CMichaelRose]

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!

https://t.co/VFoXokQP6X

[Christopher Rose @CMichaelRose]

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

[Christopher Rose @CMichaelRose]

@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.

[Christopher Rose @CMichaelRose]

@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!

[Christopher Rose @CMichaelRose]

@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.

[Christopher Rose @CMichaelRose]

@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.

[Christopher Rose @CMichaelRose]

@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

[Christopher Rose @CMichaelRose]

@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

[Christopher Rose @CMichaelRose]

@chrashwood Me watching this thread play out…

[Christopher Rose @CMichaelRose]

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

[Christopher Rose @CMichaelRose]

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!

[Journal of Proteome Research @JProteomeRes]

The latest issue of Journal of Proteome Research is live! On the cover: "Celebrating Women in Proteomics and Metabolomics"

Read it here: https://t.co/c7TgOWZfMo

[Christopher Rose @CMichaelRose]

@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).

[Christopher Rose @CMichaelRose]

@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.

[Christopher Rose @CMichaelRose]

@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.

[Christopher Rose @CMichaelRose]

@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…

[Christopher Rose @CMichaelRose]

@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…

[Christopher Rose @CMichaelRose]

@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.

[Christopher Rose @CMichaelRose]

@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

[Christopher Rose @CMichaelRose]

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!

[Denys Oliinyk @oliinyk_denys]

Very nice to see the result of my internship at @genentech out in @biorxivpreprint! If you’re intersted in diaPASEF and immunopeptidomics, check this out:
https://t.co/erUitvtb92. Big thanks to @susanklaeger and @CMichaelRose for introducing me to immunopeptidomics!

[Christopher Rose @CMichaelRose]

@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 https://t.co/VXE3Le9rWR