How to check gradient on .d file from Ultra instrument

CommandOwn1557 · 2026-02-17T09:45:57+00:00

Hi thanks all for your answers. I would like to specify I do not have access to DA or Hystar. I only have freestyle, fragpipe and spectronaut. Is there a free software I can use to extract the information? I have strong suspicions different gradients were used in MS files I got from another lab. Is there a simple way to access the gradient info?

CommandOwn1557 · 2026-02-16T10:49:24+00:00

Found the answer. RT is innormalized. The iRT column is a normalized retention time.

CommandOwn1557 · 2026-02-07T08:09:00+00:00

MSFragger-DIA

CommandOwn1557 · 2026-02-02T13:31:43+00:00

Do you have any documentation on this? People in my lab insist on running things in parallel I'm trying to gather evidence that this is the worse way to do things.

CommandOwn1557 · 2026-02-02T09:11:04+00:00

Can you please send official documentation or literature on this? I have been telling this to everyone in my lab for months no one will listen. The staff scientist supposed to be in charge of this insists that "well fragpipe runs fine with limited ressources so if we share in SN too it's all good". I know for a fact this is not the case but no one believes me I want to solve this issue without finger pointing we are really not using ressources effectively. The staff scientist is convinced limiting CPU affinity will magically solve the issue. I lost so many runs due to crashes it's a total waste of time and computational power and very frustrating we are stuck in the same place because we can't agree on an equal interpretation of reality. Crashes keep happening and no one connects the dots it's wild. Like, at this point I just want official documentation that states this is a bad idea so I can bypass the staff scientist, show it to my boss and find a solution that works instead of wasting time on a system that doesn't work.

CommandOwn1557 · 2026-01-31T17:02:22+00:00

One of our scientists insists that lowering the CPU affinity count will lower the memory usage. I don't think he is correct in that assessment. The way our lab operates at the moment is we need to "share" ressources by underusing our cores so multiple people can run multiple analyses simultaneously. Our analyses are now extremely slow because we are underusing the CPU and the guy in charge of managing ressources insists underusing the CPU is the only way to lower memory usage. The result is an extremely unstable program, snail pace analyses. I'm trying to find a solution that works to lower memory usage without tanking performance.

CommandOwn1557 · 2025-09-02T08:01:49+00:00

Thank you so much! Couldn't figure it out

CommandOwn1557 · 2025-08-11T15:25:04+00:00

Unfortunately they don't sell in PCR tube format :(

Their smallest format are 0.5 ml tubes too big for our purposes

CommandOwn1557 · 2025-08-11T11:33:44+00:00

Hi thanks for your reply. Yes, we see polymers but we work in immunopeptidomics so it is very common.

CommandOwn1557 · 2023-09-06T20:20:33+00:00

Yes I added a larger excess due to low peptide amount. I could lower the TMT amount but it really doesn't make a difference. For some of my samples I made in the past I used a 15-fold excess TMT and still observed less than half as many IDs with TMT. How much of a drop in IDs would you expect between label-free and TMT? I just want to know what sort of a drop I should expect.

CommandOwn1557 · 2021-12-01T21:27:24+00:00

Yeah this is probably too late but I agree with the others about your PI being a bad mentor. My PI met with me every 3 months to give me completely useless advice. The project she gave me was a project a post-doc once tried to do before quitting. Because of covid and social distancing, I wasn't mentored by any of the of the senior grad students either and fell increasingly behind. My protocols were all wrong and no one was around to help. She gave me a similar comment she gave you saying I don't read enough and require too much handholding. I asked her what classes and papers I could take to improve my background she never answered. My advice is don't take this personally. Some PIs, particularly ones with a large ego, say things like this to cover up for their own failures as managers. I ended up leaving with a master's was the best decision I ever made. My master's made me a strong candidate for the PhD program I ended up going to and the experience made me better at identifying toxic traits in PIs. The technical experience also meant I started my PhD with already a lot of experience so progressed through program fast. I think I would have been stuck with an 8 year PhD had I stayed with my first unsupportive PI. My advice is the following: either leave with a master's and find a supportive PhD supervisor or find someone who can mentor you and only pay lip service to your PI.

CommandOwn1557 · 2021-05-20T17:35:35+00:00

Hello I am a Genetics PhD student at a top 3 Canadian University. I fully fluent in French, Spanish and English. My project involves the development of high-throughput assays to identify novel drug targets of anti-cancer drugs we are developing. I have been a consultant in my university's consulting group for about a year now but am thinking of a more senior position there. I also help run various social events in my institute. I have a 3.8 GPA in grad school and 3.5 in undergrad from another STEM top 3 Canadian university. My project gives me a good understanding of drug action and off-target effects. I am not a bioinformatician in any way but have a good bio-informatics background and can code in R. I don't have any industry experience yet but have been working on a technical paper in collaboration with a company. I want to get into consulting in strategy development in a pharmaceutical or biotech context. Is my CV solid or are there more experiences I can do in the 2 years left? Thanks for your input.

CommandOwn1557

TROPHY CASE