Okay, I've definitely rambled about this before, but I learned from @DrJeanita (how have we not met before, I literally just go to NIST in Gaithersburg to hang out, and not just to lure people to the microbrewery across from the gate with me...but what happens pre-COVID, happens...if you don't know her, you should follow her) at the USHUPO mentoring day that it's okay to repeat really important stuff and this paper is SO SO SO important...
I'll go ahead and say it, CHROMATOGRAPHY....
And I've gotten away with pretty much ignoring it (for proteomics) my whole career. My QTrap got a decent MS/MS scan every second or so, my Orbi XL realistically got around 5 Scans/second, my Orbi Velos probably 8 scans/second and a QE Classic/Plus gets 10 or so.
If you are only getting 10 scans/second....your peaks can look like the Appalachian mountains. The resolution of your chromatography isn't holding you back. You can probably only fragment the things at the very top anyway, unless your sample is very simple.
However, as this amazing paper describes in painstaking detail -- at some point your scan speed is no longer your limiting factor -- and many of today's instruments now are at that point. What IS your limiting factor?
Ugh...as much as I hate to say it...it might absolutely be your chromatography.... We're seeing an increasing number of papers IN PROTEOMICS that are discussing chromatographic resolution, peak capacity and (...puked right on my keyboard...took a minute to replace it....) theoretical plate counts.
I can't stay on this topic much longer without thinking hard about whether I was happier the 6 years of my life I spent washing dishes in the back of a bar-b-que joint in the south that didn't have air conditioning in the kitchn, so I'm going to leave you with a really staggeringly boring powerpoint from Agilent (direct link here) that shows how you can use Algebra to understand chromatography.
If you're wondering why you can't get the results that the labs that write the papers that you hate you're collaborators carrying into your office are getting, at least part of it might be chromatography. Part of it might be that they're now famous enough that they can publish literally anything, but this sentence is probably a joke. We all know that's not how science works!