Hello Everyone,
Sometimes for cases like this, I find it helpful to make a list of potential causes: (in no particular order)
What Affects Peak Area in LC? Many of these were already mentioned above--this is only to put them in one place.
1. Injection Volume. If an injected solution on the autosampler does not experience change of any sort, injecting a greater volume will afford a larger peak and vice versa. [In this case, we believe this Did Not Occur, see above.]
2. Eluent Flow Rate. With a concentration-dependent detector such as UV, the slower the eluent flow rate, the longer the injected and chromatographed solute resides in the detector cell and the larger the apparent peak area will become. [Now, a cracked flow cell Would Alter Flow a Bit in the proper direction...but this Doesn't Seem Likely as the analyte retention time would change as well- increasing - and for everything injected afterward as well unless the flow somehow "fixed itself"? Just not likely to me, and we also think this Did Not Occur, see above.]
3. Detector Wavelength. This fellow hasn't been broached...was the measurement wavelength the same for all injections in the first LC run? Is the measurement wavelength "on-the-shoulder" of the analyte's UV spectrum as it is chromatographed? [If the wavelength varied for some reason (or the analyte absorbance, more below...) the analyte retention time would remain unchanged.]
4. Column Heater Temperature. This can affect Eluent pH--see below. [Not terribly likely, but a potential source of error.]
These Four Items Above represent the most likely Instrument-Related Culprits...at least the ones I think about. Now for Non-Instrument Culprits...
5. Eluent pH. If there is a buffer, is it of adequate concentration? Is the eluent pH constant (ought to be in an isocratic run...)? Is there are large discrepancy in pH between the injected sample and the eluent in pH (often, there can be...)? [pH may affect peak area/height, but also retention time, I don't know how likely this is, particularly as the observed behavior was transient and mid-sample sequence.]
6. Sample Adsorption to Stainless Steel Surfaces. Yes, this is Also An Unlikely Gremlin...but if the loop is SS and was a bit "gunked-up" from the previous system suitability injections, and the samples from the initial lot were, say, just a bit different in composition than everything else after it...perhaps "gunk" could have been loosened from the loop in the sample injections? [Not terribly likely, though stranger things have happened. Usually this phenomenon works the other way, lowering peak areas per analyte and requiring "priming injections" to achieve repeatable peak areas/heights.]
7. Nature of sample solvent...could it have been "different enough" in pH, organic composition, whatever, in that first lot as compared to the others tested later on to behave differently once, but not again later on? [Not terribly likely, but as in 6, stranger things have happened.]
Pretty much everyone else responding hit on all of these points--I owe apologies for "tail-gating." My small contributions are measurement wavelength, column heater temp and sample loop adsorption...as (un)likely as they are.
My feeling...whatever happened, it most likely was something unrelated to the instrument, per se. Environment, preparation of sample (after Tristanewalters), pH/pKa conflict, again sample/eluent prep (after DR and Peter Epps--was the eluent pumped from one vessel or multiple vessels, ie. "Dial-a-Mix"...could be pump behavior, just thought of that in the latter case.)