The PI3-kinase/AKT/mTOR pathway plays a central role in cancer signaling. While p110α is the catalytic α-subunit of PI3-kinase and a major drug target, PTEN is the main negative regulator of the PI3-kinase/AKT/mTOR pathway. PTEN and p110α protein expression in tumors is commonly analyzed by immunohistochemistry, which suffers from poor multiplexing capacity, poor standardization, and antibody cross-reactivity, and which provides only semi-quantitative data. Here, we present an automated, and standardized immuno-matrix-assisted laser desorption/ionization mass spectrometry (iMALDI) assay that allows precise and multiplexed quantitation of PTEN and p110α concentrations, without the limitations of immunohistochemistry. IMALDI, which combines immuno-enrichment with analysis using a benchtop MALDI-Time-of-Flight (TOF) mass spectrometer, is an especially well-suited method for translating mass-spectrometry based assays into the clinical lab. We systematically optimized the iMALDI workflow regarding sensitivity, robustness, and throughput while developing highly flexible automation protocols using a Bravo 96LT liquid handling robot. We further developed custom R scripts to improve data visualization and analysis. One hour digestion using a protein to trypsin ratio of 1:2, followed by direct immuno-enrichment for 1 h yielded high and consistent peptide recoveries. We demonstrated that the PTEN and p110α iMALDI assays can be multiplexed using both simultaneous and sequential enrichment, reducing the amount of required sample material as well as simplifying the workflow. The PTEN+p110α iMALDI assay was validated and demonstrated high accuracy for both target proteins (90-112% recovery of known spiked-in concentrations) as well as high precision and 5-day reproducibility (overall CVs of 9%) across the linear range of the assay (0.6 to 20 fmol). Lower limits of quantitation below 1 fmol were achieved. Endogenous PTEN and p110α were quantified in cell lines as well as fresh-frozen tumor tissue samples. A novel two-point internal calibration strategy (2-PIC) was developed, based on spiking two peptide isotopologues into the sample as internal standards, avoiding the need for an external calibration. We quantified endogenous PTEN in a Colo-205 cell line using the PTEN iMALDI assay, as well an orthogonal PTEN immuno-multiple reaction monitoring (immuno-MRM) method to demonstrate this technique. Excellent agreement was shown between both calibration approaches (residual standard deviation between 2-PIC and external calibration of 1.6-5.8%), as well as high correlation between PTEN iMALDI and PTEN immuno-MRM (R²= 0.9966) and good agreement between quantified amounts (0.48±0.01 and 0.29±0.02 fmol/µg of total protein). Finally, we analysed a set of patient samples from a AKT inhibitor AZD5363 drug trial using a multi-site workflow combining the developed PTEN+p110α assay with established AKT1+AKT2 iMALDI assays and untargeted proteomics. We demonstrated how the combination of targeted and untargeted proteomics approaches may be used to gain novel insights into the tumor biology of patient tissue samples. Further, we showed that the PTEN iMALDI assay has good correlation with a comparable immunohistochemistry method (R²=0.86), and that our assays can be further multiplexed, reducing the required amount sample material. Thus, we showed that iMALDI is promising tool for biomarker quantitation. / Graduate / 2022-08-12