r/proteomics

I was accepted to an analytical chemistry PhD. I did a little bit of research in environmental analytical labs in undergrad, and have been working in industry these past few years. For a year I worked in an analytical environmental chemistry lab running lots of LC/GC/ a little GCMS, and the past couple years have been working as a field service engineer on dissolution and physical testing systems for big pharma. I really would like to get involved with more advanced instrumentation and become an expert at it to get to a higher role in industry, either in pharma or at an instrument manufacturer at the R&D/ project lead level, not technician level. There is a mass spec proteomics lab at the program I got accepted to that sounds extremely interesting and seems like it has a ton of application and job prospects. Any insight into the field from the experts would be greatly appreciated, thank you.

Hello everybody, I work at a proteomics core and one issue we're trying to solve is a faster or preferably automated way to do a quick quality check of multiple raw files at once, before we search them. What currently happens is someone opens each raw file in qual browser to make sure the chromatography looks consistent between runs, before giving the "all good" to the data analysis person to search them. I appreciate any suggestions.

Hi everyone,
I’m setting up a DIA method on an Orbitrap Lumos in Xcalibur.

I want to run MS1 full scan + DIA in the same method, but I’m running into an issue:

-I can add MS1 in Experiment 1

-I can only add DIA scans in Experiment 2

-If I try to place DIA under Experiment 1, it doesn’t work or doesn’t seem supported

Is DIA actually supposed to be a separate experiment (Experiment 2) in the scan tree, or should it be possible to integrate it under Experiment 1?

Any help would be appreciated

Hello there, we have performed a pulsed SILAC experiment to measure nascent translation. And to get a greater coverage we did extensive peptide fractionation and dia a DIA based measurement on Orbital Astral. However now we are stuck at the data analysis/ search part since DIANN is not meant for fractionated datasets.

Does anybody have similar experiences and can suggest how to move forward with searching this dataset (which was quite easy in Max quant by entering peptide fractions) . without DIA and peptide fractionation we do not get a lot of H/M precursors at early time points which is where we believe our interest lies.

Any help is highly appreciated.

Hi all,

I'm fairly new to the proteomics world. I have struggled to get usable data so far and I know there are several potential weak points in the workflow. However, I want to focus on one glaring issue: about 95% of my putative proteins come back as low FDR confidence (using proteome discoverer). I have high set to 0.01 and medium set to 0.05 so it's not like it's super strict. Clearly the peptides are THERE they just are not significant enough. What would be your first troubleshooting steps? Digestion? Cleanup? LC method? Thank you in advance!!

https://preview.redd.it/1jr8y2665c1h1.png?width=1174&format=png&auto=webp&s=51211b327ca9c8015598a754a3cb929b0db1996a

Approximately 25% of 7200 noncoding open reading frames produce detectable peptides in cells with unknown function.

ok so context. ive been researching peptides for years between personal use and the people around me, and the reference situation drove me insane. you want trial dosing, you go to pubmed. you want contraindications, different paper. you want to know what the FDA actually says, third place. you want interactions or stacking data, basically nowhere coherent. most people end up trusting whatever their vendor or some forum post told them because pulling the actual literature for every compound takes hours nobody has.

so i built one. its called clinpep. 60+ peptides in it right now with mechanism, trial protocols, contraindications, interactions, citations to the actual primary sources. free. no signup wall, no email capture, no upsell. you just use it.
its at the point where i need real users banging on it to figure out whats actually missing or unclear versus what i think is fine because im too close to it. specifically.

which compounds people search for that arent in there yet. ive got my next list but its partly guesswork at this point.

whether each entry is organized in a way that makes sense to someone who didnt build it. stuff i think is clear may not be.

what data fields would matter that arent in there. interactions are thin in some entries. compounding stability is light. half life is in some entries and not others. open to whats missing.

whether the depth is right. some people want the trial citations, some people want a one paragraph summary. trying to figure out where the balance is.
if you spend any time researching peptides and want to take a look, the name is clinpep. takes 30 seconds to see if its useful for you. happy to dm with anyone who has detailed feedback or wants compounds added.

not selling anything. free is free. just trying to build something in this space that doesnt suck.

I have been working in proteomics for about 5 years.

Recently, I had a discussion with my supervisor about why proteomics journals usually have relatively low impact factors.

To be honest, I avoided submitting to these journals for years because of that. We usually preferred broader biomedical journals.

But recently I changed my mind a bit. I submitted two papers to Proteomics and one to Journal of Proteome Research.

Now I wonder if impact factor is a bit misleading in this field. Proteomics is very important, but many papers are technical, dataset-based, or useful mainly to a specialized audience.

The same proteomics study may get more attention if it is published as a cancer, immunology, metabolism, or microbiology paper instead of as a proteomics paper.

So I am curious:

Do you think proteomics journals are undervalued?

Do you avoid specialized journals because of impact factor?

For people working in proteomics or other omics fields, how do you choose where to submit?