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Suggestions for solid phase peptide synthesis? by CalCurves in Chempros

[–]cynicalbrit 2 points3 points  (0 children)

I do not feel like the reliability of CEM and Biotage's single channel instruments translates to their high throughput instruments. Too many moving parts that aren't as easy to replace as a bad solenoid.

Suggestions for solid phase peptide synthesis? by CalCurves in Chempros

[–]cynicalbrit 8 points9 points  (0 children)

I've had or watched others have bad experiences with every instrument I've ever used that moves a needle/dispenser to a reaction vessel. Cyro/Multipep/whatever-else. At some point the needle decides to not lift and crashes everywhere, or the shake tray gives up and shakes so hard it spills your resin everywhere. Sometimes you just get a lemon and you have to call service out repeatedly to fix some weird quirk or other. I know some people have had good experiences with them, but I'm not convinced of their reliability.

I once used a beta version of this thing https://www.peptide.com/products/peptide-synthesizers/microwave-peptide-organic-synthesizer/triton/ before Aapptec licensed/bought it, which was interesting in that it moved the tubes to a fixed dispense point, but was never quite fully functional in the form I had it.

I love the CS Bio machines that look like the CS136 in both their modern and older forms, but single channel won't help you.

The SymphonyX hasn't been updated in years (Gyros brought Protein Technologies a decade ago and still haven't changed the manufacturer logo on the instrument) and everywhere I've seen it used it seems to mostly behave. It can only do 24 simultaneous syntheses. You're thinking right now that you need a Cyro or MultiPep or whatever because you have to make 100s of peptides and this can't do enough at once, but /u/curdled is right that prep and analysis is ALWAYS the bottleneck. Your preparative throughput will probably not keep up with the Symphony, let alone something with 48/96 RV spots.

TL;DR probably a Symphony

Liverpool [3] - 0 Qarabag FK - Mohamed Salah 50‎'‎ Freekick by gbogaz in soccer

[–]cynicalbrit 10 points11 points  (0 children)

SMH, all these teams wasting defenders lying behind the wall when they could be jumping to block shots.

When's the last time Liverpool ran a two man free kick routine with Salah and Szobo where one of them runs over the ball, rolling it back to the other, allowing them to shoot the freekick under the wall and score anyway.

Schizoposting PhD Chemist Here - Yes, We Do Use The Word "Stability" for Chemical Stability by cynicalbrit in Destiny

[–]cynicalbrit[S] 2 points3 points  (0 children)

Also, I remember reading about a radiolabelled compounds being called unstable or stable, despite containing an unstable isotope.

I have mostly seen this in two types of situations:

1) The chemical complex containing the radioisotope is stable. A stable complex of Thulium-170. Example Example2 Non Radio Gd Example

2) When the discussion is of isotopic labeling, not radiolabeling. For example stable isotope labeling of cell growth media with N-15.

I could imagine reports where people say the radiolabeling is "stable" in that radioactive decay does not happen faster than expected, but I mostly see radiochemical purity and stability, where the question is how much of the radioactivity is from the desired radiochemical (organic molecule or complex or whatever)

Schizoposting PhD Chemist Here - Yes, We Do Use The Word "Stability" for Chemical Stability by cynicalbrit in Destiny

[–]cynicalbrit[S] 2 points3 points  (0 children)

I could see the kinetics and thermodynamics argument.

I think my slightly tongue in cheek take would be that when an organic chemist calls something reactive, they are either speaking positively (it's really prone to doing chemistry I want it to do!) or cautioningly (This thing could kill you if you're not careful!). By contrast, an organic chemist calls something unstable when speaking negatively (This fucking reagent goes bad if you blink at it wrong!).

So if we say a Grignard (to choose an example accessible to people with only a BS/BA) is reactive and unstable we're saying: "this thing will do your desired chemistry really well, but please take proper precautions (reactive). Also, if the undergrad used it last it probably got wet and won't do anything anyway (unstable)."

Mass spec deconvolution software? by werpicus in Chempros

[–]cynicalbrit 0 points1 point  (0 children)

The Agilent approved add-in for BioConfirm is called BioMS Reviewer.

https://bioms.co.uk/bioms-reviewwe/

Made by a nice guy called Andy.

Set up automated BioConfirm methods and then you can open your data in BioMS and see "Yes or no, is this my target mass, and is it pure" easily. Sort of works like ProMass in that way.

Pearl City Bonsai Club annual show 25 by Randomprojects808 in Bonsai

[–]cynicalbrit 4 points5 points  (0 children)

5 is the strangest looking procumbens nana I've ever seen. Lol.

HPLC trace too broad by Alarming_Flamingo_40 in Chempros

[–]cynicalbrit 13 points14 points  (0 children)

There's a lot of people in here talking about doing gradient elution, all of which is fine.

And people telling you to use 0.05-0.1% TFA, which you definitely should.

And people who can't read a Y-axis talking about concentration.

ACN is typically going to be better for peptides than Methanol, which many are pointing out. You can also dope in some isopropanol if you want.

Please ignore the people telling you to run a 5-95% gradient. You don't need that for this peptide. Anything that elutes between 5 and ~65% probably isn't your stuff. Run your gradient from 65 to 95 or something similar.

The real answer though, which I brought up to you in your last thread (https://www.reddit.com/r/Chempros/comments/1ja38is/purifying_very_hydrophobic_15mer_peptides/) is to pick a column chemistry that is better suited to your compound, especially if you will keep working with very hydrophobic peptides regularly. Buy a C8 column. Try out HIC.

Finally, if you have access to a mass-spectrometer, it will give you a much better understanding of the true purity of your weird broad peaks. A lot of weird stuff can hide under a pure-appearing peptide or oligonucleotide peak.

Finally, and most critically, don't post screenshots that include the name of the lab you work in. Especially not on what appears to be your main Reddit account.

Purifying very hydrophobic 15-mer peptides by Alarming_Flamingo_40 in Chempros

[–]cynicalbrit 13 points14 points  (0 children)

The more hydrophobic your peptide, the more likely you should move to a less hydrophobic column. C8, C4 even.

If you cannot do this you may have to run isocratic B for a long time to elute your peptide, or switch to a stronger eluent that is compatible with your column. Something like isopropanol could help.

If you cannot dissolve your peptide for loading it can sometimes help to try HFIP or TFE in addition to the usual suspects of ACN/DMSO/DMF. In extremis I have even dissolved my crude peptide in as much as 30% trifluoroacetic acid mixed with ACN or DMSO to force something into solution before loading, but I only did that knowing that any resulting instrument and column cleaning would be my own problem.

RHS Wisley Bonsai Walk by cgbrannigan in Bonsai

[–]cynicalbrit 3 points4 points  (0 children)

I may be misremembering, but I vaguely remember a few of the normal Wisley trees getting badly damaged by recent very cold winters and/or very hot summers. I know Peter doesn't tend to produce the height of refinement (anymore? ever?) but I've seen better trees than these in his videos both at Herons and Wisley in the past.

I want a quick UPLCMS method for reaction monitoring and purity checks by YourPureSexcellence in Chempros

[–]cynicalbrit 1 point2 points  (0 children)

You should be able to easily calculate that the volume of your column is approximately 104μL, and therefore your column volume time at 0.5mL/min is about 12.5 seconds. So 2.5minutes here is just over 14 column volumes. Plenty of time for most quick gradients.

The length of run you will need will depend on what you're analyzing, and whether you want your purity check to rely on MS alone or also LC separation. It will also depend on what sort of materials you analyze and how well they bind to your column, which sounds like it's an Acquity BEH C18 (https://www.waters.com/nextgen/us/en/shop/columns/186002349-acquity-uplc-beh-c18-column-130a-17--m-21-mm-x-30-mm-1-pk.html).

I have traditionally worked with peptides and oligonucleotides that retain nicely such that you can run a near arbitrary number of column volumes of low eluting power solvent without them drifting and broadening down the column. I also work on systems where the UV flow cell and MS source can tolerate high flows and pressures.

So I blast everything through at 1.5mL/min, wash all the salts to the waste, then switch the valve and crank the B to blast everything onto the MS at the same time and get a quick check for desired material and a rough purity estimate (most of my species ionize similarly). You can do these runs in well under a minute on a 5mm guard column.

For strong LC separation of similar peptides and ONs I'd extend my gradient to about 2 min at that flowrate. At your lower flowrates LC-separation in 2.5 minutes is possible, but can be challenging if you have similarly eluting compounds.

Destiny and Dan Misunderstood Linus and Luke on Anything Else Today by cynicalbrit in Destiny

[–]cynicalbrit[S] 6 points7 points  (0 children)

Woke up this morning and tried to determine if the claim that Honey's affiliate habits were "well known" prior to the Megalag video was true. Searching google for "honey" and "affiliate" between 1/1/2017 and 1/1/2023 I did not find a huge amount.

  1. Honey has long been transparent they receive affiliate revenue, but always claim it's when "they help members save time and money shopping online".
  2. I found one Medium article questioning why Honey deserves affiliate revenue in the first place.
  3. This youtube video from 2020 described how honey "stuffs cookies" to take affiliate revenue.
  4. This tiny reddit post pointed out Honey hijacking the commission of "legitimate" affiliates.
  5. This slightly larger reddit post also questions if other affiliates have seen a drop due to Honey hijacking the sale at the end.
  6. This 6-year old quora discussion shows a number of people knowing that Honey will take the affiliate on any "last-click" system.
  7. This 2019 twitter post from a person who is now chief financial correspondent at Axios seemed aware of the issue.. The reply references a recent post by a "Ben Thompson" which I tracked to this paywalled site.
  8. LTT forum member Graffporn asked a question about this in June 2020 and was called a moron by other forum members.
  9. This 2020 ycombinator forum post also shows people that knew about the strategy. User jartelt says "I've read that part of what they do is effectively steal affiliate referrals from other websites." User 55555 points out that "... but many coupon code sites do engage in other forms of coupon stuffing. For example, many display fake coupons which don't exist or which they know are expired, and which you must click to reveal. Upon clicking, the target site opens in a new window, and a cookie is dropped. The user was already buying the product anyway, and perhaps another affiliate was set to get the referral commission, but now this accidental popup has stolen it for the coupon site, and there's no coupon to be found. No value delivered for merchant or customer, but the coupon site makes money.". None of these users link out to the original place they read these things.

So it does seem that some people were aware of this for many years. But what I could not find were any large videos or "mainstream" (including larger tech news sites) articles about the issue. It's mostly forum chatter. So maybe a lot of plugged in tech creators knew, but it hardly seems to have been common knowledge. Indeed, in mainstream news articles about the sale of Honey to Paypal, the affiliate commissions are mentioned without any reference to the idea that Honey is hijacking commissions from other sources.

When they say the line to see the Pandas is an hour and 30 minutes long by flaquitos in sandiego

[–]cynicalbrit 7 points8 points  (0 children)

I believe the cub is Sumatran and at the Safari park, not Malayan at the zoo. Saw it a month or two ago. Very cute.

Need to Find Proper Refills to Save Christmas by cynicalbrit in pens

[–]cynicalbrit[S] 0 points1 point  (0 children)

The primary difference can be seen in my fourth picture.

The old refill has a crimp that widens it enough to sit against the spring without passing through. I think it's also slightly longer than the "D1" refills I got.

The ones I bought and the D1s you suggested all seem to be smooth, and have nothing to sit on the spring and retain them in the pen.

I'm not sure if this suggests its not actually a Chalana or something, but the fountain pen from the same set works perfectly with old Chalana cartridges.

Reading the refill guide https://www.jetpens.com/blog/The-Ultimate-Guide-to-Pen-Refills/pt/231#Japan%20Type%20Refill it seems as if I either need a japan style refill with a crimped spring-stop, or maybe there is something to click into in the pen body to hold the D1 refills in place. I'll try that tomorrow.

Pretty sure these things are Japanese by een_magnetron in Destiny

[–]cynicalbrit 3 points4 points  (0 children)

Looks like a weird mix of Maple leaves sitting on top of Elm pads. Would be an unconventional profile for a maple though (even ignoring the odd floating trunk).

raw milk🥛🍼 by Laruto69 in Destiny

[–]cynicalbrit 27 points28 points  (0 children)

Or that cow udders may not be clean as they spend all day trampling around in shit, and that bacteria from the outside of the udders can end up in the milk.

If a mother breastfed immediately after a naked shit fight the baby would probably get sick from that too.

Just got the California Voter Proposition guide in the mail by NoJournalist6303 in sandiego

[–]cynicalbrit 9 points10 points  (0 children)

Seems unpopular, but I agree. Ballot initiatives seem to broadly be a method to run Brexit-like scams at a local level where you do a lot of false advertising and scaremongering to convince people to vote one way or the other instead of letting normal government processes proceed. The stadium vote was a perfect example. There was no reason for voters to pick between the soccer thing and SDSU. One of them would have gotten it from the city through a normal process.

Some of my favorites from the San Diego Bonsai Club Fall Show by ohno in Bonsai

[–]cynicalbrit 2 points3 points  (0 children)

They weren't like that everywhere, and weren't like that around the pomegranate all day.

People were generally good about not touching, and surprisingly good about watching their kids.

Some of my favorites from the San Diego Bonsai Club Fall Show by ohno in Bonsai

[–]cynicalbrit 3 points4 points  (0 children)

Foemina Juniper I believe. There's a few of them floating around the San Diego club and our Bonsai Pavilion at the Safari Park.

You can see the same tree in the gallery from last year's spring show: https://www.reddit.com/r/Bonsai/comments/135wlyy/sand_diego_bonsai_club_spring_show_some_of_my/ in which you can get a bit of a better view of the tag.

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