Tuesday, May 31, 2011

Throw away your 8-peak beads...now.

Why is it that each booth with a new piece of hardware I walked up to at CYTO had the same set of plots 'demonstrating' how 'sensitive' their instrument is?  I can't tell you how disheartening it is after years of clamoring for a re-definition of instrument 'sensitivity' to see marketing materials littered with histograms proudly displaying 8 peaks.  What does that actually mean?  and Why do instrument manufacturers design instruments around this 'standard'?
Now, I can't totally claim innocence here.  As you can see here, and here, I do use 8-peak beads as part of my panel of instrumentation tests.  However, it's not the only test I run, and I use it more so to dismiss potential problems than single out an instrument that is performing particularly well.  One of the best things 8-peaks can tell you about an instrument is the presence of background due to laser light bleed-through, or possibly a bad filter.  8-peaks are also pretty useful as an all-around alignment bead.  Beyond that, there's not much you can infer from the resolution of 8-peak beads as to the ability of said instrument to resolve dimly stained cells labeled with a particular fluorochrome from unstained cells.  For example, the ability to resolve 8-peaks in the FITC channel doesn't mean a whole lot as to its ability to resolve dim GFP signal from negative cells.  Likewise, the inability to resolve 8-peaks doesn't necessarily mean that channel will perform poorly for a dim fluorescence signal.  Let's look at an example.
I recently had the pleasure of evaluating the 8HT from EMD-Millipore (check out the full review here).  For comparison's sake, I ran the same set of tubes on our Beckman Coulter Gallios.  After collecting the data and doing the requisite comparisons, I noticed how closely the 8-peak data matched between the two, especially in the far red channel where we'd usually detect PECy7.  The first slide below shows the 8-peak data for the PECy7 channel.  The last 3 or 4 peaks are pretty much overlapping with one another.  If we were using the 8-peaks as a metric of 'sensitivity' we'd probably conclude that these two instruments are pretty similar in their ability to resolve dimly fluorescent PECy7 stained cells from unstained cells, right?...right?

Not so fast.  If we stain capture beads with a PECy7 antibody and look at the ability to resolve the 4 peaks that represent different levels of antigen density from each other as well as a blank bead, we can better assess (emphasis on the second syllable, please) the true 'sensitivity' of the two instruments.  Looking below at this figure we can easily see that the Gallios is able to resolve PECy7 much better than the 8HT.  This conclusion matches perfectly with real-world staining examples run on these instruments.  It's obvious that if PECy7 was a pretty darn important conjugate for my panels, you know which instrument I'd be buying (if I could afford it, that is).

So, what's the take-home message here?  Well, it's simple, 8-peak data cannot be used as a surrogate for how well an instrument will detect your panel of fluorochromes.  What should you do?  Again, simple:  make sure YOU run YOUR favorite flavors of fluors on the instrument you're evaluating to give you an idea of how well it's set up for YOUR experiments.  You can certainly do this by staining your cell samples of choice, or you could use a multi-peak capture bead to look at resolution.  And if you want to quantitate this a bit more, you could extrapolate the peaks down to an area just above the blank bead to determine precisely how dim of a population you'd be able to resolve.