- by /u/Crazy-Tax-1320Hello Everyone! So I'm using a 10 kDa filter unit with 200–800 µg protein. With 200–300 ug I’m getting 40–50% peptide yield, but when I load >400–800 ug, my yield drops to 20% (or less). The filter has a max capacity of 425 µL, so for 800 ug I load 400 µL. I also notice cloudiness after trypsin digestion (as shown in the picture) What would you all recommend to improve recovery at higher loads? submitted by /u/Crazy-Tax-1320 [link] [comments]
- by /u/FactorAgreeable7518I am working with a MALDI imaging dataset for the first time. The samples were run by a vendor, and I now have the dataset, but I am new to this workflow and unsure where to begin. My background is primarily in metabolomics and proteomics, where I typically perform univariate and multivariate analyses—fold changes, volcano plots, PCA, and similar approaches. I should also note that I am not a coder by training. I would appreciate guidance on how to approach this dataset. For example, should I begin with heatmaps and cluster identification, or is there a recommended pipeline or preferred […]
- by /u/Expensive-Painter-18Hi experts, We are developing a targeted proteomics workflow on Waters Xevo G2 XS. Acquisition methods are sorted. For data analysis, I am currently using Skyline which is intuitive and very user friendly (surprisingly it reads Waters raw data with ease unlike any other open source tools). Additionally, I came across a tool from Waters – Target Lynx. I could not find any appln notes on using it on already acquired data. Does it have to be a part of acquisition method (unknown, standards have to specified before the run in MassLynx)? Also, I wonder how different will be the […]
- by /u/EvosepBioHi everyone, This Thursday we host our final webinar of 2025 that may be of interest to the community here. On Thursday, December 11, 2025 (07:00 PST / 10:00 EST / 16:00 CET), we are hosting a session on plasma proteomics workflows in translational research. Speakers: Anders H. Kverneland, PhD, MD (Department of Oncology, Herlev & Gentofte Hospital, Copenhagen University Hospital) — “Benchmark of Enrichment and Depletion Methods for Quantitative Plasma Proteomics and Their Correlation to Clinical Routine Measurement.” In recent years several preparatory techniques for enrichment or depletion for MS proteomics have been developed to overcome the extreme dynamic […]
- by /u/Redacted_1099Are there known concerns about using DIA-NN to search prokaryotic MS data? I had my PI make a comment about how he thought DIA-NN was more suited towards just eukaryotic samples. I thought I'd pass this questions through reddit after finding next to nothing through google searches. submitted by /u/Redacted_1099 [link] [comments]
- by /u/Ashamed_Lime7327submitted by /u/Ashamed_Lime7327 [link] [comments]
- by /u/zippybrownHi all — Are any core labs (academic or commercial) offering single-cell proteomics or deep visual proteomics services? I’m trying to learn what’s actually working in practice: • Which sample-prep workflows cores are using • How robust the pipelines are • What the data-analysis deliverables look like • Typical pricing/charge structures Would appreciate any recommendations or experiences. Thanks! submitted by /u/zippybrown [link] [comments]
- by /u/panay-Are there any Python packages that can match MSStats for proteomics, with things like mixed-effect models, and modelling MNAR values as censored observations rather than just imputing and treating them as real? submitted by /u/panay- [link] [comments]
- by /u/Oldtimer-proteinHas anyone tried the Axoiya phosphotyrosine kit as yet so we can compare results? We just did our first experiments with their Axobind kit and it did as they say and got a little over 10 times the phosphotyrosine peptides in comparison to our IMAC approach. Interested if others have tried it? submitted by /u/Oldtimer-protein [link] [comments]
- by /u/RumbleStrut84I do TMT SPS MS3 experiments and I was instructed by Thermo to use advanced peak determination and I didn’t think much of it. However it occurs to me that in my old tribrid we never had it activated. I read that co-isolation is an issue for MS2 experiments. Since I only do SPS MS3 for quantitation and not MS2 how much of an issue is ADP? How worried should I be about my data? Generally I haven’t noticed anything weird with my data until this most recent set that I’ve been troubleshooting. The APD came up along with the […]
- by /u/Fair-Rain3366Intrinsically disordered proteins (IDPs) make up 30-40% of the human proteome but refuse to fold into stable structures. A recent study on 72 DisProt proteins found AlphaFold3 misaligns 32% of residues, with 22% being outright hallucinations – predicting order where disorder exists. The problem: AF learned from the PDB, which is overwhelmingly ordered proteins. pLDDT confidence scores don't transfer to disordered regions. Wrote up the benchmark gap (BEACON for RNA, OmniGenBench) and what it means for measuring progress on biology's hidden half. submitted by /u/Fair-Rain3366 [link] [comments]
- by /u/DutchAnalistHi all, I’m a analytical scientist from the Netherlands and work in a pharmaceutical hospital lab. We mostly perform LC-MS analysis on small molecules. For the drug monitoring of adalimumab (monoclonal antibody) is ELISA the golden standard. I would like to discover the possibility’s of targeted proteomics for adalimumab. Is there a standard protocol for the protein cleavage using trypsine? We have no knowledge what so ever in our lab about proteomics so everything will be new (except the LC-MS system). I’ve read some papers and they have selected the unique peptide with m/z transitions. Does anyone has some tips […]
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