- by /u/No-Region-2187submitted by /u/No-Region-2187 [link] [comments]
- by /u/SilentFood2620Looking in the report.stats.tsv provided as an out by DIA-NN, how are these numbers meant to be interpreted and on what scale? Iām getting values in the 0.1 – 0.3 range but I have no point of reference of whether those are āgoodā values and the documentation isnāt super clear. Does anyone know what values are acceptable or have an idea of what values correspond to ābadā data. Any insights are appreciated. thanks. submitted by /u/SilentFood2620 [link] [comments]
- by /u/CommandOwn1557Hello all, has anyone else noticed a massive performance difference between Fragpipe 23.1 and Spectronaut 20.1 when analyzing Ultra2 immunopeptidomics data? I get almost twice as many peptides with SN20.1 using similar settings but that can't be right. Thanks submitted by /u/CommandOwn1557 [link] [comments]
- by /u/AdSuperb9486Hi r/proteomics! Quick intro: I'm Green (u/AdSuperb9486), mod of r/NextGenLCMS ā a small sub for next-gen LC-MS (Orbitrap Astral, timsOmni, ion mobility, AI tools like Koina, single-cell proteomics, biopharma MAM, etc.). Complements this sub by zooming in on bleeding-edge hardware, techniques, and AI integration. Link: https://www.reddit.com/r/NextGenLCMS/ If you're into future LC-MS stuff, come check it out or crosspost! What's exciting you in next-gen MS lately? š¬ Thanks! ā Green (mod) submitted by /u/AdSuperb9486 [link] [comments]
- by /u/KASHMlRIHi all, I am doing RNAāprotein pulldown experiments using Protein Gācoated magnetic beads to isolate RNAs associated with my protein of interest. The protein pulldown itself is well optimised and validated. However, upon RNA purification, I observe a huge background of RNA that appears to bind non-specifically to the beads or to Protein G, making any biological inference from the data impossible. Has anyone dealt with this issue or tried effective bead-blocking strategies? I cannot use DNA for blocking, as my protein also binds DNA. Thanks! submitted by /u/KASHMlRI [link] [comments]
- by /u/Routine_Arugula_5090Iāve been spending a lot of time recently optimizing a few proteomics workflows and ran into some frustrating inconsistencies with peptide quality affecting downstream analysis. It got me thinking about how much the source and verification of reagents really matters, especially when youāre trying to reproduce results or compare datasets over time. Iām curious how others here handle sourcing high-purity peptides and compounds, and whether you rely more on in-house verification or third-party lab testing. Also, for those based in Australia, do you find it easy to get reliable materials quickly, or is shipping time still a big hurdle? Would […]
- by /u/FactorAgreeable7518Hi everyone, Iām new to DIA-NN and have a few beginner questions. Iāve gone through several tutorials, but Iām still a bit confused. In many videos, people first provide a FASTA file to generate a spectral library, and then later remove the FASTA and run the search using only the spectral library. Is this step required? Or can I simply provide the FASTA file for my species together with the raw files and hit Run (i.e., library-free search)? > How can I tell when the search has finished successfully? Is there a specific message in the dialogue/log window that indicates […]
- by /u/CommandOwn1557Is there anything wrong with changing the FASTA in a spectronaut search after the analysis? Seems wrong but don't understand why spectronaut allows you to that submitted by /u/CommandOwn1557 [link] [comments]
- by /u/CommandOwn1557Hello, we are running spectronaut v20.1 and keep noticing really high ressource usage (RAM mostly) no matter what settings we use. Is there a way to cap ressources? submitted by /u/CommandOwn1557 [link] [comments]
- by /u/FactorAgreeable7518Hey everyone, Does anyone know of a free AI tool that can help quickly skim/scan research papers? I used to use Line.AI to quickly search and find articles relevant to my interests, but itās now behind a paywall. Any suggestions or leads would be much appreciated! Thanks in advance. submitted by /u/FactorAgreeable7518 [link] [comments]
- by /u/Kruhay72submitted by /u/Kruhay72 [link] [comments]
- by /u/CommandOwn1557Hello all, not sure if it's possible but I want to rerun an analysis I ran a while back in hybridDIA (DIA files with DDA library extension). Is it possible to quickly recompute this search but excluding matches to DDA? I know spectronaut allows you to recompute search results with different FASTA and FDR values. Thanks submitted by /u/CommandOwn1557 [link] [comments]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
