- by /u/Automatic_Actuary621I have 4 conditions in my experiment (A,B,C,D). If I search the conditions on spectronaut separately and then merge them in R, I get different results than if I search the 4 conditions together. It is direct DIA. I am using data at the protein level, merging the files by āprotein groupsā . Why do I have different results and whatās the best method to use? submitted by /u/Automatic_Actuary621 [link] [comments]
- by /u/thecrushahAdditionally are you doing discovery/I targeted or more targeted workflows. Iām trying to get a better understanding of the landscape. I worked on the MS side for a long time but now Iām in the chromatography space in industry and trying to get a better feel for what people are doing. submitted by /u/thecrushah [link] [comments]
- by /u/Optimal_Reach_12Is anyone familiar with the EvoSep one and how reliable it is? I was talking with a rep for a certain large conglomerate science company and they said they have seen people return them in exchange for another UHPLC. I thought one of the whole purposes of an EvoSep was and how they have single high pressure pump was reliability. I understand it could just be the rep trying to pressure me into buying their stuff so I was hoping I could get some unbiased reviews of the instrument. Thanks! submitted by /u/Optimal_Reach_12 [link] [comments]
- by /u/bluemooninvestorsubmitted by /u/bluemooninvestor [link] [comments]
- by /u/zippybrownOur core facility is looking to invest in a high-end mass spectrometer. Our primary applications are bulk DIA proteomics and PTM analysis of tissue and cell proteins, with a strong emphasis on achieving routine high proteome coverage. After demoing the Bruker timsTOF Ultra 2 and the Thermo Astral, their performance has been comparable so far. Now we're facing a tough decision and would love to hear your insights: 1ļøā£ Maintenance & Reliability: What's been your experience with the upkeep, troubleshooting, and service quality of these instruments? Are there any long-term quirks or hidden costs to be aware of? 2ļøā£ Timing […]
- by /u/PolkaGasHello all. It was suggested to me to do a sequential digest instead of a double digest for my protein. I've done a solo in gel digestion with trypsin only. In this case, I would like to ask how to process an in-gel digested sample with trypsin before doing a chymotrypsin digest. After in gel digestion, stop the reaction with TFA then dry and proceed with chymotrypsin? After in gel digestion, get the supernatant then proceed with chymotrypsin? Do I just add the chymotrypsin in the tube after incubation without deactivating trypsin? I have read the double digest protocol, but […]
- by /u/OptimalArt9172On an exemplar exam question, my professor said to assume that I eluted the peptides from the binding cleft two HLA proteins and ran them through mass spectrometry, resulting in the table below, and that āthe peptides in each group were aligned to emphasize common motifsā. I understand that the letters represent amino acids but beyond that I am clueless as to how to read this table – like, what would I even google to find info on how to read this? I have a pretty weak background in advanced science stuff (I wandered into this class from a graduate […]
- by /u/mentondeuxI am not sure why but my Perseus isn't completing Posthoc Tukey tests. On a few occasions, it has completed the activity after ~40 min, but it returns a matrix of zeroes. Is anyone else having such issues? I have done the exact process for the same dataset before, and if i run the test on the older files where it worked correctly, it does complete the test. Very confused. My workflow is: Main data (18 samples) -> Annotation rows – by categorical column, group by replicates -> log2 transform -> ANOVA (multiple sample, one way, BH FDR 0.01) ā> […]
- by /u/DoctorPeptideDespite what Google's klugey ChatGPT knock off seems to think, SpectroNaut can not process Agilent DIA data. Neither can Fragpipe. I found where Skyline listed it as Agilent compatible for DIA. I'll try DIA-NN but I think the scan header issues that make it incompatible with Fragpipe will also apply to DIA-NN. Is there anything else I'm not thinking of and should look into? I've gone down the list of the most common free stuff. submitted by /u/DoctorPeptide [link] [comments]
- by /u/CommandOwn1557Hi! I want to prepare my stocks of TMTpro (18 plex). I don't have anhydrous acetonitrile. Is it OK to dry it with CaCl2? Is there any way this can interfere with subsequent labelling steps? I will of course desalt afterwards. Thank you in advance submitted by /u/CommandOwn1557 [link] [comments]
- by /u/HamBucketsI am currently working in a lab doing research but I really want to get into bioinformatics and proteomics. My company might start doing the proteomics in house. I'm curious if something like the UCSD online bioinformatics certificate is worth my time or if I should just go back to school. https://extendedstudies.ucsd.edu/certificates/applied-bioinformatics submitted by /u/HamBuckets [link] [comments]
- by /u/shecrieswclfI am at a bit of a loss here as I canāt find an explanation elsewhere. Iām identifying peptides in collected nematode ESP and using PEAKS to search our custom prepropeptide database for any hits. Iāve had PEAKS identify PSMs but map the same PSM to two different peptides??? Same mass, same peptide sequence detected, same coverage etc etc but mapping to two completely different peptides Why? Help please ): submitted by /u/shecrieswclf [link] [comments]
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