I don't want to do the precipitation step. submitted by /u/bluemooninvestor [visit reddit] [comments ..read more

Hello! Im t trying to upload mzTab files to the PRIDE database. When i try to upload though, I face this error. Any idea on how to navigate this error? https://preview.redd.it/ncq9j4nqtgwc1.png?width=1907&format=png&auto=webp&s=522dff02f7b5cec24c3f5535f6927ff6526cc7b0 submitted by /u/Sribara [visit reddit] [comments ..read more

Greeting colleagues, I am new to the field of proteomics and i have a question regarding phosphoproteomics. I am currently reviewing some data on peptideatlas about phosphorylation of certain peptides and came across this notation: AS[167]GNYATVISHNPETK[136]. Can someone explain what the numbers 167 and 136 signify in this context? submitted by /u/DifferenceExact5414 [visit reddit] [comments ..read more

I currently have MS2 data from an agilent QTOF 6530 and am trying to run a Maxquant search on a trypsin digest of protein mixtures. I am getting very few hits and am wondering if it's due to a lower error range of the instrument as Maxquant defaults to. I even had some purified BSA that I trypsinized and ran it on Maxquant against a bovine proteome and it hit a few other proteins but not BSA. Any help in how to adjust the Maxquant search to help would be greatly appreciated. submitted by /u/Accomplished-Shop784 [visit reddit] [comments ..read more

Is is possible to Convert .wiff and .raw to .mzML in CL? Anyone had experince? I looked into ProteoWizard Linux version. However it looks like it's not compatible for Vendor-Specific data file (.wiff and .raw ) Anyone has suggestions please. submitted by /u/Drymoglossum [visit reddit] [comments ..read more

Hello everyone, I’m running some files in MaxQuant and it keeps crashing at this specific step of”digesting_proteins”. It’s very early in the pipeline but I don’t understand what it could be. I always have used the Trypsin/P enzyme parameter and it has always worked, any insights on what could be happening? Appreciate it! submitted by /u/pinderino [visit reddit] [comments ..read more

Hi all, I am currently doing a PhD in proteomics. I focus on many different things and I have obtained knowledge of instrumentation; bottom up, top down, and native MS; data analysis; and programming in R (data analysis and also small tools). I was wondering if anyone here would be able to tell me what you can do after completing a PhD as such. I enjoy research and I think I am good at it, but I don't think I can continue in academia because I want more stability... So if you someone who did a PhD in proteomics and did something else than a post doc... please let me know what and why :) Thank ..read more

submitted by /u/sam_pazo [visit reddit] [comments ..read more

Hi folks, I have already known that one protein has a phosphosite from the results of phosphoproteomics experiment. If i want to know if this phosphosite is conserved in the other 2 species' orthologue proteins, how should I do? Now, I know the orthologue proteins in the other 2 species. I'm gonna do a alignment among the 3 proteins and then how should I deduct that the other 2 proteins may have the same phsophosite? Any scoring system? Thank you in advance!! submitted by /u/AncientChemical3333 [visit reddit] [comments ..read more

I am familiar with DIA-NN. However I have been given a Linux HPC and not familiar with CL and unable to run DIA-NN since None of the Linux version comes with a GUI so its CL only. However I got to know FragPipe https://fragpipe.nesvilab.org/ in the apps available via Open OnDemand (OOD) which as DIA-NN as part of its pipeline and it comes with a GUI. ​ Is it possible to only use DIA-NN features from FragPipe? Anyone has a manual for this? submitted by /u/Drymoglossum [visit reddit] [comments ..read more