Chromatography Forum

How does one decide whether to use BPI or TIC for quantitating mass spec data? The baseline is so much cleaner with BPI, but would like to more about the two presentations before just forging ahead with something that appears better. Thanks in advance for your advice!

What's BPI? Is that a target ion quant?

BPI stands for base peak intensity chromatogram. It uses only the intensity of the most intense peak at a given retention time, contrary to the TIC which takes all ions into account.

For quantitative work, I would use EIC (extracted ion chromatograms).

You can, if you want, quantify from a total ion chromatogram, but why have a selective detector and not select? It's the mass-spec equivalent of having a diode array detector but quantifying on the total signal from 200-600nm because you don't feel like specifying a wavelength...

You should never, ever, quantify using a base peak chromatogram. The reason is best explained by an example; this example is from LC-ESI, but the situation is similar elsewhere. Imagine you inject a standard of chemical mass 500, in a system with a background ion 391 (phthalate!). The base peak chromatogram will show the intensity of 391 until 500 rises above this, and then it will switch to showing 500. As a result, the bottom of the 500 peak will be cut off, and nothing will be integrated below the intensity of 391. The worst symptom you will see is a non-linear calibration curve with the lowest points disappearing altogether. Now say we inject a real sample, and unfortunately it contains some tris buffer (122, intense!) unlike your standard. The Tris appears very shortly after injection and trails half the length of the run, now being the most intense background ion. As a result, it cuts the peak of 500 higher up! More area is removed, and the peak area that remains will give you a serious underestimate when compared to the calibration curve.

Base peak chromatograms are bad for quantification because you don't know what they're looking at at any particular time, and the ion they follow will change abruptly. They are intended only as a de-noising technique to see weak peaks. They're really good for this, though!

The good news is that if you follow Gaetan Glauser's advice and use an extracted ion chromatogram, it will be even cleaner and nicer than the base peak chromatogram.

Thank you so much! So if I understand correctly, BPI would be best used qualitatively to see if there are unknown peaks that might be just beginning to appear such as new degradation peaks or new metabolites? Then if a peak is seen and needs to be quantitated, use the extracted ion chromatogram. In our case, we don't usually know what peaks we will see (early phase stability studies) Please feel free to correct me if I'm still not getting it.

Is there a better use for base peak chromatograms?