- by /u/DoubtMysterious3059Hey everyone, I'm working on a science fair project using ssDNA aptamers and I'm stuck on the folding and docking workflow. The 3D nucleic acid folding web servers I tried keep crashing, so I'm not sure how to get a clean 3D model from a raw sequence string. Once I get the 3D structures, my plan is to use something like HDOCK to run molecular docking against my target proteins to check the binding affinity scores. Does anyone have advice on a reliable workflow or better tools I should use for ssDNA folding and docking? Any extra help with the […]
- by /u/Solid_Session_225Hi! Im struggling with my sample prep for saliva samples. I have established a high throughout SP3 digestion protocol using native saliva from cortisol Salivettes but is seems like I’m carrying some contaminants through the whole process that end up in my 7500+ Sciex Qtrap instrument which gets heavily contaminated after about 1000 injections and even gives some Q0 discharge errors. I’m running a targeted peptide method using a common C18 peptide column at a flow rate of 1ml/min with standard solvents (0.1% Fa in H2O and 0.1% FA in ACN). the whole method is 4min but I’m using a […]
- by /u/DoubtMysterious3059Hey everyone, I'm working on a science fair project using ssDNA aptamers and I'm stuck on the folding and docking workflow. The 3D nucleic acid folding web servers I tried keep crashing, so I'm not sure how to get a clean 3D model from a raw sequence string. Once I get the 3D structures, my plan is to use something like HDOCK to run molecular docking against my target proteins to check the binding affinity scores. Does anyone have advice on a reliable workflow or better tools I should use for ssDNA folding and docking? Any extra help with the […]
- by /u/popcornnzerocokeI know the FragPipe/DIA NN docs cover the basics but I would rather hear from people who actually run these pipelines daily When processing large DIA datasets with MBR, what happens after the software finishes? What does your verification workflow look like before you trust the results? How do you currently validate that the cross run transfers aren't inflating your FDR? Roughly how many hours per project does your team spend on this manual curation or refiltering? We're seeing conflicting reports on whether MBR is a reliable "set and forget" step or a major bottleneck requiring manual intervention. Curious how […]
- by /u/Middle-Box3509I am a PhD scholar in food tech department . I have been doing untargeted metabolomics for a time now for some biomarker detection. I want to learn some advanced techniques in metabolomics but i just couldnt find a proper workshop for that . submitted by /u/Middle-Box3509 [link] [comments]
- by /u/Firm-Oil6308Hi everyone, I performed DDA LC–MS/MS on mouse brain lysate (tryptic digest, non-enriched) and analyzed the data using PEAKS BSI for broad PTM searching. The software identified and mapped Ubiquitination (both lysine and non-lysine residue modifications). I reported them in my manuscript. During peer review, the reviewers raised a concern that some of the PTMs might be artifacts and suggested validating the findings using an E. coli lysate digest as a negative control. The issue is that I don’t currently have access to E. coli samples or instrument time to generate new data. So I’m looking for advice on: Where […]
- by /u/SmoothPsychology3999Most proteomics workflows still rely on multiple disconnected tools (Python, R, search engines, etc.). Do you think embedded analytical databases could become a viable backend for proteomics analysis? I’ve been exploring this idea in a recent preprint and would love feedback from the community! https://zenodo.org/records/21036067 submitted by /u/SmoothPsychology3999 [link] [comments]
- by /u/InjuryJolly7432If anyone has done in-depth IP-Top down MS on proteins I could seriously use help! I’ve isolated my POI and am trying to do to top-down MS on it but honestly I don’t know what I’m looking at/looking for. I know I need to do a full scan first to identify my POI and the m/z for it, but from there I’m baffled on what to do. The examples my colleague left for me are only for proteins approx. 35 kDa and mine is around 62! Does anyone have any advice as to what to look at/read to help me […]
- by /u/Duanqi-submitted by /u/Duanqi- [link] [comments]
- by /u/Key-Principle6254submitted by /u/Key-Principle6254 [link] [comments]
- by /u/hyperfinesplittingHi everyone, my PI suggested, mainly to save time, that I could buy individually recombinant proteins and try to reconstitute a heterotrimeric protein complex in vitro for a DSF/thermal shift assay, instead of co-expressing and co-purifying the complex. I’m a bit skeptical because of potential issues with tags, buffers, stoichiometry, stability, and whether the complex would actually form and be homogeneous enough to give interpretable data. The goal would be to test small-molecule stabilizers. Has anyone successfully done this with commercial recombinant proteins? Did it work well enough for DSF, SEC, SPR, or similar assays? Any practical advice, experience, or […]
- by /u/Connect_Switch_1026Hi everyone, I am currently a basic education teacher and I’ve recently started my Master's in Medical Sciences, focusing on neurodegeneration. I joined a newly formed research team, and while we are highly motivated, we currently lack expertise in proteomics—which is exactly the area I want to specialize in to strengthen our lab. Our research investigates neurodegeneration in the elderly. Specifically, I will be working with CSF and plasma to identify neuroinflammatory biomarkers associated with blood-brain barrier (BBB) dysfunction. My project will heavily rely on liquid chromatography and mass spectrometry (LC-MS/MS). Since I am starting from scratch in this specific […]
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