To avoid my post Xmas cheer rambling -- you should just check out this cool new QC software for heavy labeled standards in SRM experiments.
You can get the Q4SRM software here!
It has a cool logo!
Rambling you should skip:
I have a tendency to give triple quadrupole (QQQ) instruments a hard time. It's tough to go back when you've seen the power of 3 decimal places at MS1 and MS/MS. SPECIFICITY!!
I've done a couple of head-to-heads and I'm 100% convinced that even a Q Exactive Classic can still achieve higher sensitivity than any QQQ on the planet (note: in complex matrices! if you're diluting resperine in water, the QQQ wins every time. If you're studying pure reserpine go with the QQQ!!! 😇), but you need at least 100 ms of fill time to beat something like an Altis or a 6500+. That's -- at best -- 10 scans/second?.... our Altis can do over 600 scans/second... so....there are some definite advantages.
However -- SRM specificity still sucks. Wait! I read this review to help me sleep on a plane, but it ended up being awesome. I think it was this one (sorry -- its ElfSeverer.....) and the author brought up this great point -- the increase in sensitivity of QQQ devices has actually made the specificity problem worse. That when you can see lower and lower levels the chances that you will find something with an MS1 +/- 0.7 Da that also has an ion with an MS/MS fragment (or coeluting compound has an MS/MS fragment) within +/-0.7 Da gets increasingly higher! Interesting, right? Don't surplus that Quantum or 4500 just yet!
Okay -- what was I rambling about (sorry...I should put a warning at the top...).
Q4SRM! Okay -- the smart people at PNNL do a lot of specific targeted assays.
They do it this way:
1) Relying heavily on chromatography (what?? Since when does PNNL have an emphasis on chromatography being a critical component of proteomics? Where were they when we were all filling up TRANCHE with the worst chromatography of the last half century? Wait....oh...right...)
2) Putting in stable heavy labels for every peptide they quantify
3) Developing awesome software that can rapidly run QC on their stable heavy peptides as soon as the instrument has finished acquiring the spectra!
If you're going to do SRMs and you do those 3 things, I'm going to be super impressed. You've got an assay that is awesome!!
Get an SOP and get that thing out there helping people!
Is there other software you can make do what Q4SRM does? Probably! But we're all using different software packages and this is the first GUI I've ever downloaded that is specifically designed with this in mind. As light and fast as this is, you could stick to your normal data processing pipeline for your targeted quan and just keep Q4SRM on the acquisition PC to verify that everything is going according to plan.
BOOM. Massive point of data acquisition Quality Control upgrade!! And that is NEVER a bad thing.
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