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

My lab is out of c18 ziptips and I need about 20 tomorrow. However, we do have some c18-resin for preparing self-made stagetips. What would the difference be between commercial ziptips and if I made my own ziptips by placing one or two discs of c18-resin in the bottom of a 200 uL pipette tip? submitted by /u/Worsaae [visit reddit] [comments ..read more

I've read an article that structural similarity enhances interaction propensity of proteins. Does that mean we could (in theory) use tools like PDBeFold to do structural alignment of proteins and thus predict whether it is likely they will interact? A is similar to B => A in B are likely to interact. Normally when articles talk about structural similarity based approaches for finding PPIs, they use this assumption: "if two proteins A and B can interact with each other, then there may be two other proteins A′ and B′ whose structures are similar to those of proteins A and B; then it is impli ..read more