- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experimentsby /u/BioGeek​I'm excited to share our newly published paper, "InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments," now available in Nature Machine Intelligence. In this work, we introduce InstaNovo, a transformer-based neural network designed for de novo peptide sequencing. Trained on 28 million labeled spectra, InstaNovo translates fragment ion peaks from mass spectrometry data into peptide sequences with unprecedented precision, outperforming current state-of-the-art methods on benchmark datasets. Building upon InstaNovo, we developed InstaNovo+, a multinomial diffusion model inspired by human intuition. InstaNovo+ iteratively refines predicted sequences, further enhancing accuracy and reducing false discovery rates. This dual approach combines […]
- by /u/Academic-Company-215So, I just started a new job where we have a waters xevo tq absolute to run antibiotics. I have never worked work a waters instrument before and searching through the waters website is quite irritating, tbh. The colleagues who use the instrument atm had a little workshop with a waters technician on how to operate the system. But none of them is actually familiar with MS or did MS before. So when I ask them any questions they can't really answer them. I'm supposed to be the person responsible for this instrument. What is your maintenance routine in terms […]
- by /u/Front_Ad2774Can I export the peak spot table of Alignment spot view and show the peak Height of the classes? I want to convert Barchart to numeric data. Thank you !!! submitted by /u/Front_Ad2774 [link] [comments]
- by /u/sam_pazosubmitted by /u/sam_pazo [link] [comments]
- by /u/Old-Ordinary18Hello, I am analyzing human serum data for biomarker discovery of a large scale study. I did not conduct the experiments, they were done by a lab tech. The instrument used was Thermo Qexactive. The serum samples were run in 4 batches, each batch has 20 samples. Pooled QCs run with every batch. The first two batches were run in September, the third in November and forth in December. Now, across the batches, I can see an overall RT time drift of 50 seconds. I have manually verified the major peaks and they are the same m/z peaks. The batch […]
- by /u/Josky0Hello, is there a way to install xcalibur on Mac or another way to view mass spectra. RAW on Mac? Thanks submitted by /u/Josky0 [link] [comments]
- by /u/thecrushahHey all, we have a couple complex synthetic peptides where we know we have some trace impurities including some truncations. We wanted to do a full characterization via lcmsms and have already run them on an Exploris 480. I’m having trouble using Thermos software tools like biopharma finder to id the truncations. Do I need to pivot to something like FragPipe to search through the entire list of impurities we have found? Unfortunately we don’t have Proteome Discoverer so a free tool may be best here. I’m mainly interested in n- and c- terminal cleavages, internal truncations, maybe Met oxidation […]
- by /u/pataguccianerHello MS-community, our lab is thinking about substituting our rather old QTRAP 5500 and TTOF5600 (both coupled with Dionex HPLCs) with new instruments As we are already running other Agilent machines, I am thinking about getting Agilent instead of Sciex, especially when thinking about the LC systems as Agilent would also provide LC Systems This would make the interface between LC and MS less prone to errors (I hope!). Furthermore the service would be easier to organize and maybe cheaper. I never worked with Agilent QQQs or QTOFs, are they any good? Do you know how the prices for Agilent […]
- by /u/Cultural_Gur_906I'm a postdoc and soon starting my new lab. I am trying to gather perspectives that might help me decide on the kind of instrumentation to outfit my lab with. The scientific questions I've been asking will require me to do metabolomics and lipidomics, mostly targeted/quantitative. In these experiments, I will also be using stable isotope (such as U-13-glucose) tracers to measure metabolite and lipid turnover in relatively small amounts of mouse tissues. I have solid experience in the metabolite world (though, from stalking this sub, less than a many of you). I have far less experience with lipids, and […]
- by /u/Outside_Western8328I have system sutabilty standards i run on our LC QqQ systems. They generally generate stable peak areas over time. I run them before and after a pm service and then results change. Often I get a bit lower signal 20-40%. I am thinking that it might take a while to stabilise new parts like the new capillary probe. System might be to clean or new parts may need flushing. What are your routine to confirm accept system after pm service? submitted by /u/Outside_Western8328 [link] [comments]
- by /u/Upbeat_Holiday1772I use Xcalibur (v4.2) to run LCMS samples. Recently, the software started to block the submission of new sequences while it's running a sample. Basically, I have to wait for the machine to finish one sample and move to the other. Only in this period (or when the machine is not running anything) I can submit a new sequence. If I try to add a sequence while the machine is running a sample I get the following error: "Cannot open Run Sequence dialog. Close Xcalibur, and make sure acquisition service is started, then open Xcalibur." I have no idea what […]
- by /u/buggy_doctorHas anyone used mzmine for untargeted analysis of GCMS data? I’m new to using the software and find myself getting lost and frustrated with all the parameters that can be changed. Any advice would be greatly appreciated. I’ve been watching some YouTube videos but the tutorials are on LCMS or high res data so it’s not always helpful. Thanks! submitted by /u/buggy_doctor [link] [comments]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
