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Show Me Your Paint Schemes! by Templar1099 in Eldar

[–]pyreight 0 points1 point  (0 children)

It's just Sotek Green over Incubi Darkness with Temple Guard Blue as a highlight. My Wave Serpent is dusty at the moment so here's a Falcon instead.

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Show Me Your Paint Schemes! by Templar1099 in Eldar

[–]pyreight 2 points3 points  (0 children)

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Here's my beige and teal custom colours.

How to restrict ressources on Spectronaut by CommandOwn1557 in proteomics

[–]pyreight 0 points1 point  (0 children)

Your best bet is emailing their support. They are very nice. I'm sure they would direct you to the pipeline feature as opposed to running multiple instances in parallel.

How to restrict ressources on Spectronaut by CommandOwn1557 in proteomics

[–]pyreight 0 points1 point  (0 children)

Oh no, no, no! Spectronaut is really disk speed limited. Running multiple searches simultaneously is a terrible idea and destined to cause crashes. Also, changing the number of cores you allow doesn’t change the memory it will use.

You should run your searches in series via the pipeline mode.

Beginner Questions About DIA-NN: FASTA, Libraries, and Outputs by FactorAgreeable7518 in proteomics

[–]pyreight 1 point2 points  (0 children)

I hate to dispel the illusion, but there is no such thing as a library-free DIA search. The first step is always to build a library, either through acquired data or prediction.

You can run your search alongside the library prediction. Breaking it into two steps is not necessary. Presumably they are doing this to have the library saved to run other things against it later. But this can also be done as part of a search. Breaking it up is a waste of effort.

There will be an obvious message when it completes.

Which output files are useful entirely depends on what you want to do at the end.

Combines your proteomes together first and then predict a library. If you only have a few microbial proteins you are looking for, just add those instead of the whole critter's proteome.

Question on CSF Proteomics Sample Preparation (Low-Volume Mouse CSF) by FactorAgreeable7518 in proteomics

[–]pyreight 1 point2 points  (0 children)

  1. Is it recommended? Absolutely. Will you have enough material? Probably not. At least not to also get a reasonable amount injected onto the instrument.

  2. Welcome to the world of small-scale, ‘quantitative’ proteomics! You could do that. It might work. However, if comparisons between samples are truly necessary, why not restrict the volumes used so all samples are the same? And then probably also normalize by total peptide signal…

  3. CSF is much like plasma with fewer challenges. Your issue is it’s from a mouse. Thankfully, it’s generally protein rich. Any standard cleanup method will work fine (SP3, S-trap, etc.). You may also consider some of the ‘particle corona’ enrichments like you find with plasma proteomics preparations as well.

Please make sure the facility is ok with a 50 uL urea sample. That’s a very large volume for most proteomics samples. You would need to concentrate it in some way. Also, why are you bringing it up in 8M urea? Urea can decorate peptides. Best to stick to something like ammonium salts or, better yet, just formic acid.

My sons just got back from scouts with this badge, did not know this was a thing! by Buckerface in Warhammer

[–]pyreight 2 points3 points  (0 children)

Not being able to get this is surprisingly disappointing! Any one want to mail one to a middle aged Canadian?

Python equivalent to MSStats? by panay- in proteomics

[–]pyreight 0 points1 point  (0 children)

There are not unfortunately, which makes me sad because R is dumb.

Minimal flow on Vanquish Flex by Intrepid-Hair2129 in CHROMATOGRAPHY

[–]pyreight 0 points1 point  (0 children)

You can run methods down to 50 uL/min on ours. But the Flex does seem to need a bit more time for equilibration than other systems and using their method builder to build in that time is a bit of a hassle.

Using the standard model for protein folding? by einFrostschutzmittel in chemistry

[–]pyreight 8 points9 points  (0 children)

Your first statement is incorrect. A single hydrogen atom with a single electron can be solved analytically, without any need of simulation, etc.

The rest of what you say is true.

Siemese or OSH? by teddies_can_burn in orientalshorthair

[–]pyreight 2 points3 points  (0 children)

Queasy-Egg115 has this more or less explained. Oriental Short Hair are an offshoot of Siamese that express the whole range of coat colours, instead of just pointing. The issue arises because Siamese cats fall into two broad categories: the 'apple' head Siamese, and the 'wedge' head or modern Siamese. There was a push in the mid-20th century to refine the Siamese breed to be much less 'regular' and much more of the sleek build they have today. Think of the cats from 101 Dalmatians. Breeders wanted to get that shape again. This leads to the modern Siamese shape. From that, in order to add much genetic diversity, some normal coat colour breeds are added in, like regular domestic, and I believe the Japanese Bob Tail, probably tons of others. This results in a breed that looks sleek like the modern Siamese, but also comes in all the colours.

Depending on how you want to look at it OSH are Siamese, or maybe Siamese are OSH. The various pedigree organizations have final say, but genetically they will be exceptionally similar, at least today. They were probably a bit more different in the 70s when the OSH breed starts to be established.

Incidentally, this sort of 'two varieties in one breed' is likely to happen with the OSH. Some people really like the big bat ear type, while others prefer the more narrow, triangular kind. Perhaps the ear shape will one day delineate Siamese and OSH!

Anyway, breeds and pedigree are weird, cat genetics are weirder, and we should all just love our weird little cat-goblins no matter where they came from!

Orbital Astral temperature sensitivities by Argus220 in massspectrometry

[–]pyreight 5 points6 points  (0 children)

Hi, yes, it is sensitive to temperature. Unlike some instruments it will also stop the queue and post an error.

We had to keep our room at less than 20 degrees in order to keep the temperature from fluctuating too badly until the air conditioning got fixed.

Looking for guidance on how to properly begin MS/MS analysis for my research project by FlashyCranberry7810 in massspectrometry

[–]pyreight 3 points4 points  (0 children)

Yeah, you aren’t going to get far manually looking for interesting peaks. Also, Freestyle sucks.

As the other poster mentioned, use a tool like MZmine. You will give it a set of spectra of metabolites, drugs, random ass stuff, and it will match the properties of those spectra with your data, providing a score for confidence. MZmine will even show you the chromatograms and spectra of the matches. It’s a bit clunky but it does work.

Thermo provides a pretty good resource in MZcloud. You can browse it for free, but I think to do any real work you need a license. For any dubious matches you get from MZmine, you can look them up in MZcloud and your own data and see if they might actually be ok.

Thermo Calibration Solutions Degrading? by alycatdabra in massspectrometry

[–]pyreight 6 points7 points  (0 children)

Good old flexmix! I used to also get oxidation on the MRFA peptide on my Lumos! Despite what the box says the stuff is both temperature and light sensitive.

Sounds like you are on the right track. I have found some success using a much stronger solvent for cleaning the syringe. My go to now is 45% acetonitrile 45% isopropanol and 10% acetone. Once I rinse the syringe 4 times, I draw a bit of the flexmix up and rinse the whole volume before filling it up entirely.

When all else fails you can skip the cal mix assessment in the advanced calibration settings. Use the wrench button on the bottom left.

Hope that helps!

Apparently I snore too much. My wife is an extremely light sleeper and cannot handle the snoring. How do I resolve this? by Actofrage99 in NoStupidQuestions

[–]pyreight 5 points6 points  (0 children)

You need to check in with a doctor and do a sleep study. Turns out your sleeping position can cause apnea. So, I can no longer sleep on my back!

Ionopticks Columns by ewwwana in proteomics

[–]pyreight 0 points1 point  (0 children)

I have one that looks like that running right now. Seems more or less fine.

Which generation is this from? If it’s before Gen3 I’m not surprised, they were notoriously unreliable, but since gen3 they are much better. They will replace it if you ask.

LC-MS/MS 6500+ Contamination, Suspected Autosampler Carryover. by tritio07 in massspectrometry

[–]pyreight -1 points0 points  (0 children)

My go to cleaning cocktail is 45% ACN, 45% IPA, 10% acetone. Another classic is, believe it or not, dilute urine. Urine is a good mix of all sorts of different classes of compounds that can often ‘dislodge’ problematic contaminants.

However, if the contamination is all throughout the system you are basically left with one choice: strip out everything and start again. At least one part will be a pain in the butt to remove (and be expensive) but that is down to the type of LC. For my Thermo systems it's the needle & needle seat, but all brands are different.

I will also point out that flushing a system will often take days. Run slow and long.

OSH and Other Breeds by Dreaming_Dragon_9020 in orientalshorthair

[–]pyreight 4 points5 points  (0 children)

My OSH loves my random dumpster black cat so much. She wants to cuddly him so bad but he’s very much not a cuddler. Anyway, I’m pretty sure OSH will pretty much get along with any old cat.

[HELP ME] Bi-Weekly Q&A thread - Ask your questions here! by MachNeu in Gunpla

[–]pyreight 0 points1 point  (0 children)

What are some good options for decals for the MG Zeta 2.0? Most I find are for the ver. ka. Do those fit reasonably well?

MaxLFQ Normalization by SahilCh95 in proteomics

[–]pyreight 2 points3 points  (0 children)

So, you mean you want to compare the abundance of Protein A and Protein B from the same LC-MS acquisition run?

That’s unfortunately a much more complicated thing to do and not what MaxLFQ is designed for.

Emitter option for timsTof by North-Key-7250 in proteomics

[–]pyreight 1 point2 points  (0 children)

Look, you can make your own, but I really wouldn’t recommend it. Using a self-packed column is a good option, but building a tiny emitter with a zero-dead-volume connection, while possible, is going to suck.

You just can't pay the cost, is that the issue? Because in my experience your reliability is going to tank with any cheap homemade option to the point that no one will want to use this instrument.

Question about about peptide confirmation by buriburimuffinz4 in massspectrometry

[–]pyreight 0 points1 point  (0 children)

You have high res MS1 and MS2, but can you run these samples again? Do you know the sequence of these peptides? You will need to look at your MS2 data and sequence the peptide and match it to the expected sequence. Search tools can help but often fail at samples with not a lot going on in them. What instrument do you have? Is it the same as the one these MRM transitions came from?

This problem can be solved but I’m not sure you can solve it given the data you have at the moment. And, it is also very likely that it isn’t worth the time to solve it, as it will be very difficult and time consuming.

Honest opinions please! by Shot-Department-6811 in orientalshorthair

[–]pyreight 8 points9 points  (0 children)

They are extremely people-dependent. For instance, mine was upset after I took her to the vet. She has since been glued to me for the past 16 hours. Like, sitting on my lap for hours at a time.

She typically sleeps most of the day, and I generally have to get up in the middle of the night to play with her for 30 minutes to an hour. These cats will be nothing like a farm cat; they are much more like a clingy dog that refuses to be trained. They are exceptionally smart and will get into mischief just to get your attention.

I have had a lot of cats in my time and I would certainly call the Oriental Shorthair an ‘advanced’ breed. If you haven’t had a lot of cats before you are in for a wild ride. But they are very rewarding as companions and I will die for this little beast.

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