- by /u/sidharth45What could be the reason for this error? I have run some samples in lcms orbitrap to analyse the mebatolic changes in mcf-7 after treatment. Since I’m very new to this field, I got no idea what went wrong. So pls help me understand what is the problem here submitted by /u/sidharth45 [link] [comments]
- by /u/sidharth45Hello all, like I said before in my previous post Im pretty new to omics technology. I have run some samples in lcms and I have tried to analyse the data using mzmine. But I am getting an error message as shown in the image attached. Please help me what to do and what might be reason for this error. submitted by /u/sidharth45 [link] [comments]
- by /u/WaviLabHas anyone made the transition from a triple quad LCMSMS to an Orbitrap for non-targeted PFAs testing? I plan to open a PFAs testing lab in the next year. Any advice or suggestions? The number of compounds an orbitrap can test for makes it a very lucrative investment for PFAs labs. I have multiple orbitraps & will probably only use 1-2 in my lab. If anyone is in the market for an orbi, I can supply one for $40k-50k under market price. I hate these companies that rip scientists off with huge markups. submitted by /u/WaviLab [link] [comments]
- by /u/Few-Conclusion2888Hi, I have new samples, which are from small piglets small intestent. The samples were collected using a buffer. Im trying to make a protocol for the preparation for NMR metabolic analysis. There is like no literature about this so I mainly used protocols for fecal sample preparation. If someone had some better idea, let me know. Thanks The protocol (it is a bit vague. Dont get into specific volumes, just the principle): Centrifugation at 14,000 × g for 10 minutes at 4°C or vortexing for 10 minutes (to remove solid residues). Addition of extraction solvent: MeOH/H2O 1:1 (recommended for […]
- by /u/0dd1ti3Greetings all. I have an idea for a project, but I’m not quite sure of the methodology for identifying unknown metabolites(or simply detecting their presence). I suspect my favorite protein (MFP) binds metabolites. I regularly affinity purify MFP and have successfully used LC-MS/MS to identify proteins complexed to MFP. I do not know what specific metabolites bind, but suspect a specific structural class. I’m not sure how to process my affinity purified material to ensure I do not lose metabolites or what is required to prepare a metabolite containing sample for analysis. Most of my contacts look for a very […]
- by /u/sidharth45Hello people. I’m a newbie in the field. I’m trying to learn metabolomics and I want to get a hands on analysis sample data using different free tools to analyse omics data. Can anyone please share me their csv files or any other files so that I can try metaboanalyst or MSdial etc. I don’t have any seniors who are working on metabolomics or who has worked on metabolomics and I don’t have any guidance for the same. Pls pls pls help me. 🙏🏻 submitted by /u/sidharth45 [link] [comments]
- by /u/atatime90Hello! I'm working on spectral matching of small molecules. I'm exploring different tools, but currently we're interested in the GNPS platform. I occasionally run into the problem of having large m/z errors (ppm of hundreds to thousands!) in library matching. There are no problem with ubiquitous fatty acids and nucleosides (almost 0 error), but I always have some trouble with polyphenols, terpenes etc. I'm using an Orbitrap LC MS/MS instrument. What do you think are the factors affecting the large mzerror? Do you think the level of separation (gradient elution method) in the LC has something to do with it? […]
- by /u/Drymoglossumsubmitted by /u/Drymoglossum [link] [comments]
- by /u/YoeriValentinI'm not sure if this is allowed, but we're such a small community and this isn't for profit (and hopefully educational), so I think it should be fine. I made an hour long presentation on why most polar metabolomics isn't reproducible or useful. This is specifically about human/animal samples (so, not plants). The picture I paint isn't very positive, but I feel like the information in this presentation should be common knowledge to anyone working in the field (Edit: I mean that in the sense that I want this to become common knowledge, not to make you feel stupid if […]
- by /u/cepera_228Hi everyone, I'm working on a project involving metabolomic data analysis using MS-DIAL, and I’m facing some challenges with annotating my metabolites to the KEGG (C00…) format. Specifically, I have a dataset with the following: Here’s a sample of my data: Unnamed: 0 Alignment_ID Average_Rt(min) Average_Mz Metabolite_name 1 Pos_3090 6.114 191.10234 "2,6-Diaminopimelic Acid" 2 Pos_3297 7.616 198.08911 "N,N-Acetylhistidine" 3 Pos_10614 2.791 377.14484 "(-)-Riboflavin" 4 Pos_1600 5.976 144.10246 "(2r)-6-Methylpiperidine-2-Carboxylic Acid" 5 Pos_3456 2.493 202.10730 "(E)-1-(4-Methylquinazolin-2(1h)-Ylidene)Guanidine" My goal is to: Map each metabolite in my dataset to a corresponding KEGG compound ID (C00…) if possible. Obtain a list of pathways for each […]
- by /u/pluvio7856Can anyone help me in analysis of metabolomics data. I used UHPLC-HRAMS technique on plant samples submitted by /u/pluvio7856 [link] [comments]
- by /u/Adventurous-Job2217Hello there, I am plant metabolomics recently working on human samples. I experienced GNPS based molecular networking with plant extracts as my samples. I would like try it more but this time, for human samples metabolome. I am working on plasma/serum and urine samples. I am looking into doing FBMN, MS2LDA, etc. but not sure on what analysis parameters to use for human samples. Would there be a big difference? What would be some differences I have to take note and how do I execute it in terms of analysis? Anyone who would be open and down for a discussion […]
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