Monday, June 24, 2019

LIMS (laboratory information management systems) for mass spectrometry labs!

At ABRF this year I talked a lot about a SOPs and LIMS and why I loved they are critical to our future development as a field.

Laboratory Information Management (LIMS) systems are maybe starting to take off now, in some form or another, after a couple of false starts?  I think proteomics changed way way too fast -- 2D-gels were still cutting edge not all that long ago and are mostly a niche technology now. A lot of coding went into technology that aren't our central pipelines anymore.

What's a LIMS? Well...the word means a lot of different things to a lot of different people, but this is how the old Johns Hopkins Clinical LIMS worked when I was there a million years ago.

1) Samples come in and are barcoded
2) Samples only move to a new place when a new person (tracked person) scans them and moves them to a new location (sample collected. sample arrives at new location)
3) Samples are only processed by the strict criteria in the computer (multiple choice options  -- no creativity allowed).
4) Sample data is reported out into the LIMS as it is achieved
5) Most of this data is directly uploaded to the computer by the instrument
6) The operator verifies this data is correct
7) The data goes into permanent encrypted storage that is only accessible by the appropriately credentialed parties.

This is obviously a lot trickier for some assays than others. What was the CRP level? The total albumin, etc.,? That's a lot easier than -- "what was the relative shift in the PARPylation level across the entire proteome normalized against the global level?" Extra steps involved, but it's the same stuff.

Whoa! Here is a great review that is better than what I'm going to write. You should check it out instead!

Do we have LIMS options now? I think so, and I hope that we'll have more. (Let's stick to global untargeted first)

In no particular order check out Proteios.

First you'll think -- that paper is 10 years old! Well, here is a paper where it was used just a few months ago!

Another great one (more focused on the data management side, as far as I can tell) is msLIMS.  It runs via a really slick Java GUI that you can get here.

Okay -- for something completely different (and something you have to buy, no idea whatsoever the cost, but there is a 30 day free trial, disclaimers over there somewhere... -->) check out this LabKey thing!

It appears to be a more full-functioning LIMS with available Skyline/Panorama support and direct integration!

Back to the stuff for global -- here is another one from the rush around 2010 to get platforms out (MasSpectra) that has been seen in the literature as recently as the last few years (Bonus, it's a 2014 malaria flagella paper that I've never seen before!!)

Are there more? I hope so! But this is a decent start and more than I thought I'd find today!!

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