- by /u/RumbleStrut84Someone just opened up nice big containers of milk protein and BSA and weighed them next to me while I was prepping my buffers for proteomics sample prep. I found some clean, unused glassware and went to another clean lab to re-make everything. Normally I would not bother cleaning glassware for proteomics and just get new supplies, but I need to save money. Does anyone have a reliable method for cleaning glassware to remove protein contaminant? The containers would be used for making buffers to prep samples for proteomics so I am trying to avoid detergents. submitted by /u/RumbleStrut84 [link] […]
- by /u/Educational-Goal-736A question for the proteogenomics community here: I have been trying to create a custom protein database to identify variant peptides from DIA data downstream. So far, I tested both ProteoDisco (R) and pypgatk (python) without success. Do you have any suggestions for tools that I could use to create a custom protein database using a VCF file or a VEP annotated VCF containing variants of interest? Thanks! submitted by /u/Educational-Goal-736 [link] [comments]
- by /u/CommandOwn1557Hello, I would like to visualize all the entries in the FASTA I used for my proteomics search as a dataframe in R. Anyone know how to do this? submitted by /u/CommandOwn1557 [link] [comments]
- by /u/No_Championship_5269Recently, I recieved a project that is add a small molecule tag in Purified protein from my senior fellow student. I need to compare modification ratio in different catalyze condition. Can I use the formula Ratio = Intensity(modification)âž—[Intensity(modification)+ Intensity(non-modification)] for proportion approximately? submitted by /u/No_Championship_5269 [link] [comments]
- by /u/writinglover0101Hi, I am trying different target ID strategies (PELSA & photocatalysts w/pull down); however, I have been having trouble seeing any integral membrane proteins in my protein lists when either submitting samples to mass spec cores or now trying to do the mass spec runs myself on a tims-TOF. I'm pretty sure my target is a GPCR but as for which…. that's what the experiment is for. For PELSA, this would be a bottom-up proteomics approach that is basically a modified LiP-MS experiment. So far I have tried lysing cells with PBS with 3x freeze-thaw cycles, but I would like […]
- by /u/Status-Ad5185Hi, I am new to proteomics and looking for some insight. My lab has started experiencing a problem with Waters Sep-Pak where after we have eluted from the cartridge and dried down there seems to be a significant amount of silica from the cartridge passing through into our samples. Has anyone else been experiencing this? We have only noticed with the 50 mg cartridges- not 100 mg/500 mg/1 g yet. We only received the order Dec 2024 so i assume it cannot be expired. Only thing is the packet has been opened for some time. submitted by /u/Status-Ad5185 [link] [comments]
- by /u/RumbleStrut84Typically when I process cells for proteomics I do it within a a few days after harvesting so they are only briefly stored at -80C. Someone gave me cell pellets that I warned I wouldn’t get to for 3weeks. I’ve kept them at -80. Do you think they are still OK? submitted by /u/RumbleStrut84 [link] [comments]
- by /u/SahilCh95Hello, I am a little confused about the MaxLFQ normalization method and was hoping someone in this community could clear some of this up. To the best of my understanding MaxLFQ intensities are typically used to compare the intensities of specific proteins across different samples runs, so for example it should be used to compare the relative abundance of a specific protein across your test and control samples. However, can it also be used to compare the intensities of different proteins in the same sample run? Or would something like an IBAQ be more appropriate in this case? submitted by […]
- by /u/MammothManner6208I am looking for comprehensive courses and tutorials on proteomics data analysis using Python and R, with a particular focus on applying machine learning models for data modeling. My main interest is in developing approaches to model microbiome proteomics data, integrating computational methods with biological insights. submitted by /u/MammothManner6208 [link] [comments]
- by /u/North-Key-7250Hi, we have recently inherited a timsTof 2 from another lab, who has been using the Ion Optics CSI column all the time, but I can’t seem to find good alternatives, except the Captive sprayer from Bruker, which is overpriced of course. I would like to replace emitter rather than using the integrated emitter columns. Anyone has good and budget suggestions? Thank you submitted by /u/North-Key-7250 [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 August 28, 2025 (16:00 CEST / 10:00 EDT), we are hosting a session on “Streamlining Translational Proteomics Workflows”. Speakers: David Ezra Gordon (Emory University) — applying high-sensitivity LC-MS to map immune regulation, including cytokine signaling and T cell exhaustion. Nigel Kilty Kurgan (Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen) — talk details coming soon. The webinar will focus on practical workflows in translational proteomics, with emphasis on immune regulation and robust LC-MS methods. Registration & details: […]
- by /u/Accomplished-Ad2792Hi everyone! Is it possible to compare Olink and TMT data? Although I don’t know proteomics well, I understand that they are veryyy different so sorry if this is a stupid question! I’ve found several proteomics datasets on my topic, but they are all very different (TMT, Olink, DIA, etc) and there’s actually none that are the same method. I know it’s a long shot but I thought I would ask before I have to give up entirely. submitted by /u/Accomplished-Ad2792 [link] [comments]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
