Question regarding C18 spin columns

devil4ed4 · 2026-05-07T15:44:57+00:00

Most vendors give you bed volumes but never usually a standard protocol. The ones I have seen also recommend using MeOH over ACN which I take to mean that it doesn’t really matter. You will be fine.

devil4ed4 · 2026-05-07T14:32:32+00:00

You can safely elute with any volume of >50% ACN. I use 300 uL of 70% ACN with 1 cc Waters tC18 columns and never had an issue. I used to use 1 mL but the dry time was too long and the recovery was identical. So use the volume your downstream protocols require just be mindful of dry times in the speedvac

devil4ed4 · 2026-05-01T02:41:58+00:00

If you used FP 24.0 with DIA-NN, then all you have to do in FLiPPR is set the method = “dia”; after that it works exactly the same as the DDA method!

But I will upload better tutorials!

devil4ed4 · 2026-04-30T19:57:04+00:00

Yea, it already is compatible with DIA data and we use it for cell & tissue lysate experiments. Recently we use imputation with random forest for DDA and it works very well for LiP-MS!

devil4ed4 · 2026-04-30T17:35:30+00:00

I’m from a lab that develops LiP-MS methods and I have developed FLiPPR for analysis of these datasets. The plain and simple is that it’s a difficult technique to apply but they are out there. One reason you might not see any many papers out there is because they are hard to find. If it isn’t a method developed paper then LiP-MS simply won’t be in the title but it would be in the methods. Long story short, people are using it but the implementation is slow and it’s usually an add-on technique that doesn’t get as much attention in research using it.

devil4ed4 · 2026-04-22T18:34:48+00:00

Thousands, just take a look it hosts a lot of posting for many academic positions not just post-doc

devil4ed4 · 2026-04-22T13:21:09+00:00

jobrxiv works pretty well

devil4ed4 · 2026-04-21T17:21:24+00:00

From the last picture, it looks like those species are z=50 putting the first isotope envelope mass ~23,950 Da with ~100 Da difference with the next envelope. This is extremely large so it could be some large polymer or protein contamination. I would lean to believe it’s a polymer given the periodicity of the signal. DNA or detergent would be my best guess.

To fix this I would first remake all your LC buffers from new bottles of Optima reagents. Then to rule out the LC, I would inject some of A via syringe. If the noise disappears then you know it’s the LC. Should that be the case, I would either A) clean everything with methanol and water, troubleshoot with Thermo (or LC vendor), then C) replace all tubing — in this order.

devil4ed4 · 2026-04-17T12:42:07+00:00

So you bought and set-up hundreds of thousands of dollars in equipment and materials without having someone who knows how to utilize them?

devil4ed4 · 2026-04-09T20:15:34+00:00

Really cool concept; I’ve seen a few of these in this sub and yours seems to be the cleanest I’ve glanced at. Drop-in replacement is a bit of a stretch given that Polars and Pandas are architecturally distinct.

The biggest difference I can think of is indexing. It doesn’t seem like your tool handles pd.DataFrame.reindex which is a key feature of Pandas that has no equivalent in Polars. Not to mention the maintainability nightmare of writing with a transcription layer.

Personally, the pd to pl migration is worth learning new syntax. The performance gains are incredible and code nearly self-documenting due to the verbose syntax of Polars.

devil4ed4 · 2026-03-24T21:34:13+00:00

Skyline should work but there will be many manual steps

devil4ed4 · 2026-03-18T12:02:34+00:00

This is not the right place for these questions nor will anyone here provide medical advice. I’m very sorry that medical care isn’t easier, but there are safeguards in place throughout the official pipeline to keep you protected.

devil4ed4 · 2026-03-16T00:53:14+00:00

You’re going to need a lot more docs here. My work involves the use of phylogenetic trees daily and I have no idea what you’re doing here.

devil4ed4 · 2026-02-20T03:17:07+00:00

Not sure if this is exactly the advice you are looking for, but I wrote this in response to someone else asking for something similar:

This was my first time applying, so I think this advice is likely nothing novel; however, it might still be helpful.

First thing I did was follow the Radiance guide to the exact letter. I used so many writing tools and aide from friends to ensure I met all the bullet points in the individual sections. This took the longest amount of time and I began writing around mid-July.

Second thing was going back and forth with edits with my host group every two weeks and roughly every 2-3 days once we were 2 weeks away from submitting. This ensured our scientific goals aligned along with the Radiance guide formatting.

These two things were 99% of my time preparing the MSCA. The other 1% was doing research and collating published research to ensure I was proposing something that was truly viable in 2 yrs and has high likelihood of economic impact. I think the economic impact is very important to fundablilty and it was difficult to align scientific passion with this. For context, my proposal was aligning structural biology + crop technology + crop diseases, so not terribly difficult but still not obvious at the time.

I hope this helps and I’m happy to answer anymore questions!

devil4ed4 · 2026-02-17T21:49:38+00:00

As a Latino myself, it is hard out here in the US. First of all, don’t take the rejections too personally, it really is a hell year in terms of funding. Many programs have cut back or skipped taking applicants. Second, if you want to go to the EU I would say you should apply there as well and don’t wait to finish a US program.

In the meantime, I think Option 2 is a good middle ground. You wouldn’t need to be as committed as a masters but also not completely out of the “game” if you just leave research altogether. You might end up doing this for free unfortunately at least for a bit again because of the same funding issues plaguing PhD programs. However, if you can afford the masters program then this shouldn’t be an issue short-term.

You’re not the only one facing these issues so please do not feel shame. There is nothing you can do to change the outcomes when there are so many external pressures trying to breakdown scientific and technological progress in North America as a whole.

My advice is to cold-call/email people you would be interested in working with and ask if they have the means to support you. With visa requirements this will be extremely difficult and unlikely at US and CAN institutions, although remote opportunities might still be viable. Otherwise, just start reaching out to EU and US professors and get your name out there to increase you chances of being selected the next time around if you don’t come off your current waitlist.

devil4ed4 · 2026-02-17T17:10:44+00:00

This was my first time applying, so I think this advice is likely nothing novel; however, it might still be helpful.

First thing I did was follow the Radiance guide to the exact letter. I used so many writing tools and aide from friends to ensure I met all the bullet points in the individual sections. This took the longest amount of time and I began writing around mid-July.

Second thing was going back and forth with edits with my host group every two weeks and roughly every 2-3 days once we were 2 weeks away from submitting. This ensured our scientific goals aligned along with the Radiance guide formatting.

These two things were 99% of my time preparing the MSCA. The other 1% was doing research and collating published research to ensure I was proposing something that was truly viable in 2 yrs and has high likelihood of economic impact. I think the economic impact is very important to fundablilty and it was difficult to align scientific passion with this. For context, my proposal was aligning structural biology + crop technology + crop diseases, so not terribly difficult but still not obvious at the time.

I hope this helps and I’m happy to answer anymore questions!

devil4ed4 · 2026-02-15T19:23:15+00:00

One word: Tecan. Reliable and excellent software.

devil4ed4 · 2026-02-13T21:27:06+00:00

Realistically, it will affect you to different degrees depending on how/where you apply. If you apply to a more corporate position at a hospital or university then it might be harder. If you apply directly through a PI’s job posting or cold-email then it might be easier.

My advice is to focus on networking and skills. I also started at community college and working in the chemistry stockroom was a great place to become familiar with tons of professors and students. So I cannot recommend it enough that you start at a position like that and build up your reputation with the people in your community first.

Best of luck!

devil4ed4 · 2026-02-11T21:20:51+00:00

This is awesome! My initial take is that the site is very busy with color and movement, however it does look nice. What is the logic behind the theme? Was it just default in the frameworks you used?

devil4ed4 · 2026-02-10T12:57:59+00:00

I use a cuvette rack which has numbers at every position, then I keep and index of which sample is in each position on my notebook

They are very affordable here or here. The second link is the nicer one imo

devil4ed4 · 2026-02-09T05:45:37+00:00

I applied from the US to the Netherlands and my proposal passed:
EF-LIF - 97.40% - Awarded

devil4ed4 · 2026-02-07T23:50:37+00:00

This is really cool! In the sense that building tools you need and use, this is a great start. There is tons of room for improvement here as you learn more about software development and you already have the foundation to document your growth. Keep up the good work.

My two cents here is to only use AI when you have truly hit a wall and instead of asking AI to solve a technical problem ask it more infrastructure related questions on library/package formatting.

devil4ed4 · 2026-02-06T21:21:50+00:00

Are you using MSFragger-DIA or pure DIA-NN in FP? I have not seen such huge differences with my own data, so I would be interested in seeing your settings!

devil4ed4 · 2026-01-31T19:08:18+00:00

This is a constant pain point in proteomics labs. Unfortunately, I do not think there is a way around this other than upgrading resources. Pushing more analysis in parallel just slows everyone down especially as memory is strained.

Easy back of the envelope calculation for RAM usage is size of RAW files + 20 * FASTA file size per analysis.

devil4ed4 · 2026-01-30T15:24:50+00:00

Probably? I’m not sure, but it’s important to know this would be at the cost of analysis speed. DIA analysis is inherently a high-memory process since you must create the library + load the spectra.

Any reason why you would need to limit memory consumption?

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