/r/proteomics/

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  • Still seeking new moderators for /r/proteomics and Proteomics discord server
    by /u/tsbatth
    Dear Proteomics community, As the title implies, we are need of a few more moderators for the channel as well as moderators for the "Proteomics" discord server. As before, we are still open to those interested in "stylizing" the subreddit visually. Please contact the mods and we can provide you with the details. Link for the Discord (currently not operational): https://discord.gg/BuHMnNcAqZ submitted by /u/tsbatth [link] [comments]
  • Can someone share a copy of this paper on JPR?
    by /u/bluemooninvestor
    Mass Spectrometry Acquisition and Fractionation Recommendations for TMT11 and TMT16 Labeled Samples Kindly DM me if you can share. submitted by /u/bluemooninvestor [link] [comments]
  • Looking for a cart for Vanquish Neo
    by /u/godgabba
    Hi All, As the title states I am trying to find the most ideal cart for the vanquish neo. We currently have a McMaster-carr AV cart. I like the design of it, and the fact that it has outlets, but the problem is it doesn’t support the weight of the Neo(the cart supports 150 lbs, the Neo is 145, but with reagents on top it surpasses 150). Does anyone have any recommendations for carts that have outlets that can support the Neo for under 500 bucks? Interested to hear what others with the system are using. Thanks submitted by /u/godgabba […]
  • SPEED Lysis Technique Advice
    by /u/JoeCylon
    Hello, I'm working on implementing the SPEED (Sample Preparation by Easy Extraction and Digestion) technique by Doellinger et al and I could use some advice from anyone who's gotten it working with tissue. First I'm wondering how well it scales up? I'm aiming to work with tissue pieces in the 50-200 mg range and wondering if anyone has run into issues with over-diluting after the 10x Tris neutralization step. Secondly I could use advice on protein concentration measurement with this technique. My lab is standardized on BCA so if you have experience with SPEED + BCA I'd appreciate any specific […]
  • Confusing SPS MS3 data
    by /u/RumbleStrut84
    Hi, I'm very new to Reddit so please hang in with my long post! I have been doing TMT SPS MS3 for several years now and I just came across some odd behavior in which every other channel has higher signal (3-fold) compared to the neighboring channel. I attached an image blocking out the names of the samples except for the numbered replicate, but they are in order from 126 to 131c. The more fractions I collect the less it stands out, but the trend is still there with some proteins. I explored a few possible causes: heat map of […]
  • AI model deciphers the code in proteins that tells them where to go
    by /u/Vailhem
    submitted by /u/Vailhem [link] [comments]
  • Bunch of RTS SPS MS3 doubts. Guidance requested.
    by /u/bluemooninvestor
    Hello everyone. Here is the scenario. I am learning proteomics and this forum has helped me immensely. I am trying to do TMT based proteomics, and with everyone's guidance in this sub, I have been able to ateast get TMT labeling done properly (99% on an old instrument). Now I am trying to outsource the acquisition to a facility with Thermo Eclipse. Unfortunately, they don't know about SPS, RTS and stuff (no idea why they acquire MS2 on eclipse). Neither is the Thermo guy of much help. Hence, I am requesting the experts in the subreddit to please guide me […]
  • Thoughts on MaxLFQ Minimum Ions
    by /u/Practical-Buy-2439
    I’m analyzing DDA data with Fragpipe. What is generally the acceptable minimum number of ions for MaxLFQ? When I was being trained 10 years ago with Maxquant, it was instilled in me that a minimum of 2 ions were required. But I’m seeing papers in reputable journals with only 1 ion. Thoughts? submitted by /u/Practical-Buy-2439 [link] [comments]
  • [R] how can I find patterns to distinguish between MCAR and MNAR missing values?
    by /u/Automatic_Actuary621
    submitted by /u/Automatic_Actuary621 [link] [comments]
  • Hi, I'm new to proteomics, is there any way I can run dia-nn on mac os?
    by /u/WoodpeckerActive
    submitted by /u/WoodpeckerActive [link] [comments]
  • Astral data processing
    by /u/mai1595
    Astral peeps, would love to know your experience with the data size, processing softwares, PC config and the time it takes. Thanks for the help! submitted by /u/mai1595 [link] [comments]
  • Analysing LFQ proteomics data
    by /u/nxcxlxs1
    Hi all, I have a few basic questions on analysing some LFQ proteomics data I recently generated for the first time. I am doing the analysis using PERSEUS, where I loaded the LFQ intensities, log-transformed them, removed proteins not identified in 3 samples in at least one of four groups, and imputed the NaN values with the default PERSEUS parameters. To assess sample similarities, I did a PCA, clustering and correlation between samples. Is it most appropriate to do this on the LFQ intensities per sample per group, before performing the log transformation / filtering / imputation of the data? […]

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