Cancer is a complex, life threatening disease, existing in many forms. Here, we present a study comparing plasma samples from cohorts of bladder and lung cancer patients, with healthy controls using a high-throughput targeted OMICS workflow. This workflow allows for rapid screening of various compound classes using a single LC-MS platform. A known level of a labelled analogue from each compound class was added to each sample. The level of each analyte was then estimated using its ratio to this. Data was collected for 18 samples (6 controls; 6 bladder cancer; 6 lung cancers). QC’s (a pool from all samples) were acquired every ninth injection. In total, 206 injections were performed (runtime = 22hr). 128 compounds were measured, generating a %CV <20% for the QC samples: 80 proteins, 20 acylcarnitines and 28 amino acids. Valine-d8 (amino acid spiked in samples) is used as an example to illustrate the consistency of response across the whole study (CV= <5%). Pair-wise comparisons using a t-test were performed on each compound class. The amino acid sarcosine was demonstrated to be up-regulated in both lung and bladder cancer samples; the acyl carnitine Octenoyl-carnitine (C8:1) was down-regulated in bladder cancer subjects; and protein analysis highlighted various differentiating species, including Apolipoproteins. This data demonstrates the ability of this targeted approach to highlight potential markers in a high-throughput manner. Method development was unnecessary, and results were obtained in <24 hours. The next step would be to validate the markers by performing a more statistically rigorous study.