- by /u/Fit-Purple324Hi people I ve been converting raw files to mzML with thermorawfileparser, tellling it to return me indexed mzML files. I noticed that the indexed files are huge compared to the non indexed, and their size is pretty close to the original raw files. So which one should i use for diann (v2+)? Thanks a lot for the help. submitted by /u/Fit-Purple324 [link] [comments]
- by /u/Plastic-Fan-6849Hi! So, I'm currently researching the protein contents in breadfruit (A. altilis), which there is not a lot of previous proteomic data on. I have run multiple jobs on FragPipe using jackfruit (A. heterophyllus) and breadnut (A. camansi) databases, and every single time I get keratin proteins?? Keratin is most definitely not found in breadfruit… I have no idea how to move forward to properly elucidate the identity of these keratin proteins. What should I try? Thanks!! submitted by /u/Plastic-Fan-6849 [link] [comments]
- by /u/ewwwanaI need a sanity check – is this what the emitter of the Aurora Elite normally looks like? Is this packing material creeping into the emitter tip? I’m 12h apart from Australia so progress with their customer service is painfully slow. After only 24h of using this column it’s unusable due to extremely high backpressure. I just ran standard peptide samples and two lysates, it surely cannot be dirty yet. But alas I am troubleshooting. submitted by /u/ewwwana [link] [comments]
- by /u/EvosepBioHi everyone, We’d like to share an upcoming webinar that may be of interest to the community in here! On October 23, 2025 (16:00 CEST / 10:00 EDT), we are hosting a session on Deep Visual Proteomics. Speakers: Melissa Klingberg (Max DelbrĂĽck Center, Spatial Proteomics Group, Berlin) — “Exceeding 100 Spatially-Resolved Proteomes per Day: An Optimized Ultrasensitive Tissue Proteomics Workflow.” Spatial proteomics (SP) enables precise mapping of protein abundance, localization, and interactions in tissues, offering deep insights into cellular function and disease. We co-developed Deep Visual Proteomics (DVP), integrating high-resolution microscopy, AI-driven image analysis, and laser microdissection with deep proteomic […]
- by /u/bluebottl3Would anyone be interesting in having their risk assessed? It would be a mail-in test, so fingerprick (no needle required). We are a potential spinout from the university of Oxford. Looking at what people think https://www.ox.ac.uk/news/2024-08-08-proteins-carried-blood-offer-new-insights-ageing-and-age-related-disease-risk https://www.oxcode.ox.ac.uk/news/blood-proteins-may-be-able-to-predict-risk-of-cancer-more-than-seven-years-before-it-is-diagnosed Or even the organ health/age? https://pubmed.ncbi.nlm.nih.gov/38915561/ submitted by /u/bluebottl3 [link] [comments]
- by /u/RendertheFatCapHey all, my lab has been on boarding proteomics to help support multiomics efforts in the group. One thing I see as I've been doing sample prep testing is that some papers recommend centrifuging down cell suspensions before a more thorough lysis step and some don't bring it up at all. What do you recommend? Should I try and resuspend the insoluble bits, so I'm sampling them as part of the proteome? I tend to perform a more thorough lysis after a flask harvest at 60C with some detergent/chaotropes, so I figure I've got to be putting some of those […]
- by /u/bluemooninvestorI am using Pierce™ MS-Compatible Magnetic IP Kits Protein A/G https://www.thermofisher.com/order/catalog/product/90409 What happens if I directly go to in solution digestion and don't bother to remove the antibody? How much difference would it make? Please help. Trying this for the first time. submitted by /u/bluemooninvestor [link] [comments]
- by /u/sam_pazosubmitted by /u/sam_pazo [link] [comments]
- by /u/Strawberry_beagleHi everyone, I’m fairly new to proteomics and have some questions regarding data normalization in Perseus. I’ve been following some of the MaxQuant Summer School recordings on YouTube, which have been really helpful, but I still have a few doubts—especially around normalization steps and when they’re necessary. From what I understand: 1. Normalization starts within MaxQuant, especially when doing LFQ analysis, so in many cases, further normalization in Perseus might not be needed. 2. However, it’s common practice to check data distribution (e.g., using histograms) before doing downstream analysis like t-tests, to decide whether additional normalization is required. That said, […]
- by /u/BioGeekI'm excited to share our new preprint on Winnow, a framework for model calibration and false discovery rate (FDR) estimation in de novo peptide sequencing. Deep learning has made de novo sequencing (DNS) increasingly powerful, unlocking several proteomics applications previously out of reach. But a key gap remains: DNS models often produce miscalibrated scores, and we’ve lacked principled ways to estimate FDR. Without that, results are hard to trust or compare across models. That’s the problem we set out to solve two years ago. With Winnow, we introduce a post-processing calibrator that rescores model outputs using spectral and prediction features, […]
- by /u/Past_Noise6573Hi all, need your suggestions. While preparing sample from micro S-trap, I calculate the right amount of SDS but made a mistake while adding them, and ended up with 21% SDS in my sample. I realized this later after preparing them. Obviously I'll not run these in MS now, but looking for suggestions if there is a way to rescue those samples. submitted by /u/Past_Noise6573 [link] [comments]
- by /u/Disastrous_Archer404submitted by /u/Disastrous_Archer404 [link] [comments]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
