- by /u/Expensive-Painter-18Hey guys, need once and for all understanding of terms in MRM/PRM methods. Confused with dwell time, cycle time and duty cycle. Pls correct me if I am wrong DT is time spent in acquiring a single transition (each precursor fragment pair) CT is total time taken to acquire within area under the curve (peak sampling) DT is where I struggle and I am unable to differentiate with CT. This said how do you optimise to get the best intensities? Have seen the impact of collision enegies and but apart from that which of the above paramaters influence the most? […]
- by /u/Crazy-Tax-1320Hello Everyone! I’m growing Huh7 PNPLA3-WT cells, and I’m getting low protein yield in the BCA assay. I grow the cells until they reach 90% confluency, then lyse them using activity buffer with protease inhibitor, phosphatase inhibitor cocktails 2 and 3, and PR-619 in DMSO. I scrape the cells well, add ruptured beads, vortex, place the lysate on the agitator, centrifuge, and collect around 700 µL of lysate. I repeated this three times at different passage numbers. During the first attempt at passage 4, I obtained 700–900 µg of protein, but at passages 10 and 11, I only obtained around […]
- by /u/P_O_Y_AI regularly use MS for proteomics but recently found another approach using ONT's technology. https://www.nature.com/articles/s41586-024-07935-7 What is the field's thoughts on it's potential and practicality? Thanks! submitted by /u/P_O_Y_A [link] [comments]
- by /u/Evening-Room-8586Does anyone have any information about PhosphoSite Plus stopping their academic licenses? Is anyone's account still active for their site? Currently working on a project that would benefit from accessibility to their database, any information would be useful. submitted by /u/Evening-Room-8586 [link] [comments]
- by /u/bluemooninvestorsubmitted by /u/bluemooninvestor [link] [comments]
- by /u/EvosepBioHi everyone, We’d like to share an upcoming webinar that may be of interest to the community here! Tomorrow November 20, 2025 (07:00 PST / 10:00 EST / 16:00 CET), we are hosting a session on targeted proteomics workflows. Speakers: MargrĂ©t ĂžorsteinsdĂłttir & Finnur Freyr Eiriksson (University of Iceland) — “Advancing Protein Biomarker Quantification: Performance Evaluation of the Evosep Eno – Waters Xevo TQ Absolute LC-MS Platform.” This presentation will showcase a robust, high-throughput LC–MS platform integrating the Evosep Eno with the Waters Xevo TQ Absolute for precise and reproducible quantification of plasma protein biomarkers. The workflow demonstrates exceptional sensitivity, […]
- by /u/FactorAgreeable7518I am currently optimizing a workflow in which I aim to begin with 10% ACN in biofluid (samples having 10ug of protein in BCA estimation) on a 10 kDa filter, collect the filtrate (degradome), and then resuspend the retentate (the top part on 10KDa) in 8M urea buffer to proceed with the standard proteomics preparation (reduction, alkylation, trypsin digestion, and quenching). After trypsin quenching in the retentate , I aim to mix the filtrate (degradome where I assume to have endogeneously processed peptides) with trypsin digested peptides and run them in LCMS (DDA). The overall objective is to identify microbial […]
- by /u/Expensive-Painter-18We analysed cell lysate from HEK 293 cell line on Waters Xevo G2 system in nanomode and same sample was also provided to Sciex facility where equal load was tested on Zeno ToF. The difference in number of IDs is huge! Xevo with 150 mins run time could barely ID 1500 proteins while Zeno ToF with 30 mins run time easily churned out 3500 protein IDs. I know Xevo is an older model but even QE Orbi which is released in almost same year as that Xevo will easily outperform it. Where do Waters systems suck? I see good MS1 […]
- by /u/kinder_brzI’m experienced in basic data analysis but new to clinical omics integration — especially linking omics data with patient outcomes, treatment groups, and survival/time-to-event statistics (Cox models, hazard ratios, etc.). Could you recommend any books, GitHub repositories, YouTube tutorials, or online courses that teach how to integrate proteomics data with clinical data and perform downstream statistical and bioinformatics analyses? Preferably R-based resources, but Python ones are also welcome. Thanks in advance! submitted by /u/kinder_brz [link] [comments]
- by /u/MagnusLocoHi, I would like to know how can (if I can) compare the proteome of species A, B and C (same genus), given that they were identified and quantified individually. I ran an Orthogroups analysis to find the proteins orthologs. Do you think I could draw "direct" comparisons, like "protein X has 2 log fold change in species A compared to B" ? submitted by /u/MagnusLoco [link] [comments]
- by /u/CoolBanana0Hi all, Looking for some hardware/feasibility advice. Our institute recently aquired a new Thermo Vanqish (flex, not neo) and Orbitrap Exploris 120 with the hope of doing proteomics. I've spent most of my PhD making proteomics probes and doing in gel flourescence but requiring collaborators to aquire proteomics data for us but we are now looking to move things in house. Unfortunately we do not have the budget/expertise for setting up a full proteomics lab. Looking for some advice to see if the equipement we have is capable enough to get some meaningful data. From what I can see: The […]
- by /u/RumbleStrut84I have always been collecting MS2 of digests before TMT labeling using an orbitrap-ion trap MS2 method with FAIMS on a tribrid mass spec. I have a very small coIP sample and I need to do a simple ID and have been asking around what methid people prefer. the couple of people I spoke with seem to prefer an OT-OT method without FAIMS, but I get far fewer IDs with a HeLa digest with such a method. I understand that the MS2 spectra would be higher resolution, but if you want more depth is there a strong reason why people […]
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