The increasing focus on high throughput sample analysis has led to the common practice of using simplest sample preparation method possible (i.e. protein precipitation) and shortest sample run-time possible. This means that there will be two aspects of compromise: the first compromise is made between sample cleanliness and sample preparation speed since protein precipitation does not provide very clean final extract; the second compromise is made between peak separation and run-time, meaning that sometimes overlap or co-elution of some peaks has to be accepted. The first compromise may lead to matrix effect, which is caused by co-eluting endogenous substances such as phospholipids. The second compromise can result in analyte effect, which is caused by co-eluting analyte(s). We have encountered the issue of matrix/analyte-mediated ion suppression in multiple preclinical and clinical pharmacokinetic projects during bioanalytical method development/validation or biological sample analysis of many small molecule drugs. As these matrix/analyte effects could occur in different situations with different \"syndromes\", sometimes it can be easily overlooked, leading to unreliable result, poor sensitivity, and prolonged assay development process. To increase the awareness of this important issue, in this paper we presented two real case examples on signal suppression caused by either endogenous phospholipids or co-eluting analyte.

Two fish parvalbumin models were established to study relationships among matrix effect, extractability, and thermostability during in vitro immunodetection using two parvalbumin-specific monoclonal antibodies (3E1 and PARV19). Our results illustrated that matrix-induced thermal instability of parvalbumin was due mainly to physical (hydrophobic effect) and chemical (thiol-disulfide interchange) interactions. The addition of sodium dodecyl sulfate (SDS, surfactant), β-mercaptoethanol (reducing agent) or ethylenediaminetetraacetic acid (EDTA, metal chelator) during sample preparation could not only increase the extractability of parvalbumin but also enhanced its immunodetection. Our findings demonstrated excess EDTA completely chelated Ca2+ in parvalbumin and rendered it undetectable using PARV19 (a Ca2+-dependent antibody). Overall, our resulted showed that matrix effect on in vitro analyte quantification cannot be underestimated. Any false negative or positive results could lead to severe or life-threatening allergic reactions.

In order to choose a sensitive, selective, simple, rapid, cost-effective and reliable analytical method for a given complex sample, a strategy was proposed for the evaluation of an analytical approach to determining multi-pesticide residue in complex agricultural product matrices, using leek as an example. In this work, the matrix effect of most of pesticides were in the range of -50% to -90%. A simple thin layer chromatography (TLC) was used to evaluate the effect of cleanup. The results agree well with that of matrix effect described above. More than 91% of the investigated compounds achieved recoveries were in the range of 70-120%. The limits of detection and limits of quantification were in the range of 0.1-3.5ng/g and 0.4-11.5ng/g, respectively. The strategy can be used to analyze multi-pesticide residue or related chemicals in diverse agricultural product matrices to provide technical guidance in choosing an analytical approach.