How to save your samples before it’s too late!

Picture this: You’ve planned your experiment, collected all of your samples and you’re ready to run them on your LC-MS. Time is tight, so you get your samples through as quickly as possible, making the best use of the time available to you. Finally, it’s complete and your data is ready for analysis – great, so far so good. You start analysing your data in your preferred software — or simply what’s available to you — but after several painstaking hours of frustrating analysis, you’ve realised that something’s not quite right. After a bit of investigation, you find that your data just isn’t usable, due to sample running problems at the time of acquisition. Time to beg for some more time on that LC-MS… assuming you have some sample left, of course!

Sound familiar? Wish there was a quick and easy way of checking your data for problems while you’re still running samples, so that any issues could be identified and rectified quickly to prevent wasting time collecting “garbage” data? Here’s how Progenesis can help:

Quality control comes first in Progenesis

The first stage of the workflow in Progenesis is Import Data. Here, the raw data is imported and immediately visualised in the form of a 2D ion intensity map.

The ion map for a single LC-MS run viewed at the Import Data screen

It’s this ion map that can be used to quickly spot a multitude of common sample running problems. We recommend installing Progenesis on the acquisition PC and checking the quality of your data every set number of runs using the ion intensity map to prevent any nasty surprises during the analysis.

If you’re worried about needing an additional Progenesis licence for this QC, have no fear: importing data into Progenesis doesn’t require a licence, so you can–

Wait a second! That’s a really important point that’s worth repeating:

Importing data into Progenesis doesn’t require a licence.

This means you can install it on as many PCs as you like without fear of delaying anyone else’s analysis (or even having to make an initial purchase of the software!). You’ll also be pleased to hear that as you’re not using any of the more powerful analytical processes and algorithms involved later in the Progenesis workflow, you can carry out this QC step on a reasonably basic PC.

Don’t just take our word for it

If all of this sounds too good to be true, here’s what Dr Paul Langlais from the Research Division at the Mayo Clinic (Arizona, US) had to say about the early QC in Progenesis:

“Progenesis is label-free quantitative proteomics at its easiest. What surprised me is how much I was able to improve the quality of my mass spec runs, using the 2D map feature combined with the charge state distribution analysis…

What nobody realizes is how powerful Progenesis is in analysing LC and instrument method design. I’ve completely redesigned everything. I look at other people’s .RAW files and I see how much they could use the 2D feature alone.”

And when you consider that Progenesis supports data from a wide range of instrument vendors as well as several generic file formats, this makes it a suitable and important resource for pretty much any LC-MS lab.

Spread the word

Did you find this article helpful enough to share with other researchers like yourself? If so, click here to share the tip on Twitter – if we can save even one experiment together, it’ll be well worth it!

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