Wednesday, May 11, 2022

Where can I get help with proteomics questions?!?


This list isn't meant to be comprehensive, but I think maybe it could be helpful -- I'll add it as a permanent link over there --> somewhere. 

Let's start with where do I go when I need help with something? Well...over the last 19 years of doing mass spec type stuff I've developed a network of contacts that I go to when I'm stuck. If you are interested in this post chances are you don't have an ill-advised tattoo that someone prominent in this field told you was a great idea after you shared a completely responsible amount of scotch that they  feel just a little guilty about and that you can leverage for help extracting MS1 XICs for the rest of your career. 

Have you tried Twitter? It is probably still alive right now since that smelly emerald mine heir that has tricked everyone into thinking he started Tesla and SpaceX hasn't yet taken over and tried to run that into the ground. There are a lot of helpful proteomics people on it! 

Did you know there is an active proteomics reddit page? That's a great place to put questions, although r/biochemistry and r/bioinformatics have larger subscriber bases and frequently feature proteomics sample prep and data processing questions respectively. 

Questions on the sample prep side? Okay....that's tougher, unless you are using a commercial solution. I use S-Traps, so when I need help I bug the support team at Protifi. If you are doing SP3 via the PreOmics stuff, bug them! If you are doing prep on the cheap, maybe try Reddit? 

Software? This is much much better and I cannot stress this enough, use the Github support pages and Google groups for your software of choice! 

MSFragger has a level of support that is bordering on absolutely impossible to fathom

MetaMorpheus is just as insane...almost 600 closed issues...?....

On this topic, anyone who has a Github up will get an email if you bug them. If you're using the code they published -- bug them! 

MaxQuant has a series of Google groups that include a section on basic mass spectrometry questions in general!

Commercial software? This is the best part of commercial software, they have support people! Don't let them sit around bored, contact them! 

Need help with a method? Have you tried Not everything is in there, but over the last 5 years or so I've tried to convince other people to put their methods there. Maybe it will happen one day.  I'm wonder if the reason the project hasn't really taken off is because most people with mass specs aren't confident enough in their ability to use an instrument to feel okay making them available.  So... it is about 98% methods that I have personally made and since I have experience with, and access to, just about everything, the resource still plods along, gets downloaded a lot and I occasionally get positive feedback about it. 

Is your question about mass spectrometry hardware? This is great. Call or email the instrument vendor! Don't have a contact? Do this! 

1) Figure out who your local sales person is 

2) Tell them you have questions! 

This might actually be a useful application for LinkedIn. I bet your sales rep is on that thing! 

Because not everyone knows this, this is largely how the system works. Your local sales rep is paid just about enough money to not lose their home. Not much more. The manufacturing company wants them as desperate as possible to sell instruments. If you are sitting there with your instrument (even an old one) and you are struggling, you don't have time to write a great grant to buy a new one, do you? Even if you do, you probably will buy something else thinking you'll struggle less with it. You struggling with your hardware is bad news for your vendor. Contact your sales rep. 

They will, almost without fail (unless they've had a bad couple of years and are working nights at a hospital or spending all their time applying for jobs) get you help. You probably have local applications people and you definitely have applications support people somewhere. Now, depending on how greedy the vendor company is, when you buy that Fusion 4 instrument, your sales rep will either have a party or a really big party, because even 1% of that instrument is a pretty good day for most people in science, so it works out for everyone somehow. For real, bug them, they'll be excited to hear from you.

I feel like I forgot something else I wanted to add....maybe later! 


  1. I don't know why such a good forum closed its door:

  2. is good as well