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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 26d

Ok, thanks everyone. Right now I am trying open search. I have some instrument time next week, so I'll try an collision energy curve then too as I still have some sample from this experiment.

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 28d

Does anyone have advice for how to handle large (>500 Da) synthetic mass adducts for proteomic analysis? I have evidence of this chemical modification in my samples via western blot, but I am struggling localizing it via Orbitrap. #teammassspec #proteomics #chemsky

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 26d

But I'll wait till later at least.

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 26d

9am on a Saturday morning and it's a long weekend for me (took Monday off because I'm seeing Kali Uchis on Sunday), but I feel drawn to looking at the status of my Fragpipe and my LCMS QTOF runs...

an older woman in a blue shirt is standing in the woods

Alt: an older woman in a blue shirt is standing in the woods

media.tenor.com

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 28d

I use Fragpipe with MS Fragger precursor tolerance at +/- 5 ppm and fragment tolerance set to 5 ppm, trypsin with 2 missed cleavages, Percolator with a FDR of 1%.

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 28d

Not sure if it could be interfering with tryptic digest or ionization, but I get a decent number of IDs in my analysis, just hard to reconcile the strong modification signal via western with the few modified peptides via LCMS.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · 28d

Does anyone have advice for how to handle large (>500 Da) synthetic mass adducts for proteomic analysis? I have evidence of this chemical modification in my samples via western blot, but I am struggling localizing it via Orbitrap. #teammassspec #proteomics #chemsky

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Sep 1

I think your favorite biomolecule reveals a lot about your personality. Almost like the biochemical MBTI.

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Sep 1

#BiochemSky sound off below ⬇️ , what is your favorite biomolecule? 🧬 #SciSky

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Aug 7

One of the most devastating facets of the human experience is this disease. Unpredictable, evasive tragedy. I'm hopeful when I think of mRNA vaccines and such, but the heterogeneity of this disease gives me the greatest fear.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Aug 7

I saw a reddit thread today about the best molecular biology papers that people have read, which led me to this paper. Extremely eloquently written, but every time I think about cancer deeply I am floored by it's complexities.

www.cell.com/fulltext/S00...

The Hallmarks of Cancer

After a quarter century of rapid advances, cancer research has generated a rich and complex body of knowledge, revealing cancer to be a disease involving dynamic changes in the genome. The foundation ...

www.cell.com

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Aug 7

I'm using these beads to enrich full length proteins.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 31

Takara's magnetic resin looks really promising, but if anyone has any reviews, I'm willing to hear them before I purchase it 😊

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 31

Hey #phosphorylation folks! I've played around with some commercially available titanium dioxide resin for peptide-level enrichment, but I want to look at some phosphoproteins via western blot. What's the most cost effective way for protein-level phospho-enrichment? #chemsky #scisky

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 26

Definitely not as user friendly as I would hope, but I'm thinking I finally figured out a way to screen a library of ~350 hits against a one target using this tool... Activating my educational license for the pro tier also made things run more smoothly.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 25

Trying out Alphafold for the first time. Let's see what the hype is about.

an older woman in a blue shirt is standing in the woods

Alt: jamie lee curtis

media.tenor.com

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 15

I'll look into this!

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 11

Not to mention that I've saved *so much* storage space thanks to analyzing from mzML instead of RAW.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 11

Don't tell PD, but I have quietly switched all of my analyses to Fragpipe. What an extremely powerful software. I'm often amazed at the sheer quantity of information I can get using Fragpipe. Thanks to everyone who recommended it.

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Apr 5

Extremely niche troubleshooting request, but is anyone familiar with implementing MSFragger in Proteome Discoverer? A few of us keep seeing these error messages, but none of us are tech savvy enough to decode it. Every time we "solve" it, it happens again.. #proteomics #teammassspec

$System.IO.FileNotFoundException: Could not find file 'D:\nick (temporary local analysis folder)\HeLa Pulldown\HeLa Pulldown\temp1593\50nM_OspF_02.pepXML. File name: 'D:\nick (temporary local analysis folder)\HeLa Pulldown\HeLa Pulldown\temp1593\50nM_OspF_02.pepXML' at System.IO._Error.WinlOError(Int32 errorCode, String maybeFullPath) at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean FromProxy, Boolean useLongPath, Boolean checkHost) at System.IO.FileStream.ctor(String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize) at System.XmI.XmIDownloadManager.GetStream(Uri uri, Credentials credentials, IWebProxy proxy, RequestCachePolicy cachePolicy) at System.Xml.Xm|Ur|Resolver.GetEntityUri absoluteUri, String role, Type ofObject ToReturn) at System.Xml.Xm/TextReaderImpl.FinishInitUriString0 at System.Xml.XmIReaderSettings.CreateReader(String inputUri, Xm|ParserContext inputContext) at System.Xml.Xm|Reader.Create(String inputUri) at MSFraggerPDv30.PepXMLReader.ReadPepXML(String PepXMLPath)|$

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 11

I don't know who told me that everything will be stagnant for weeks then suddenly things will rapidly fall into place, but I feel like I'm landing there right now. I was reading a list of GO terms and I had a moment of revelation I hadn't felt for a very long time in my career.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 11

After a very long time of feeling like I've been banging my head against the wall because my PhD project has felt like a barren fishing experiment, I finally feel like a have at least one hypothesis that I can directly test to learn about my enzymes of interest.

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 11

Thanks everyone for input! We tried a hard reset on the system, and it's seemingly restored function... 🤞🏻

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 10

Extreme rookie question, but our lab just had a power outage and now our #Orbitrap Exploris 240 is not acquiring any data. Here's what our HeLa digest standard looks like before and after outage. Anyone know what might be going on? #teammassspec #proteomics #chemsky #scisky

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 10

(Coupled with a Vanquish neoLC btw)

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 10

We tried changing the column, but that didn't change things. Other internal standards in our lab also give this absence of signal...

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 10

Extreme rookie question, but our lab just had a power outage and now our #Orbitrap Exploris 240 is not acquiring any data. Here's what our HeLa digest standard looks like before and after outage. Anyone know what might be going on? #teammassspec #proteomics #chemsky #scisky

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 1

Fortunately most of us were doing things that could go in the fridge or freezer until we were able to come back. Sadly one student was in the midst of seeding cells and had to bleach them... but she'll be able to seed again on Wednesday :)

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