Metabolite profiling by mass spectrometry (MS) is an area of interest for disease diagnostics, biomarker discovery, and therapeutic evaluation. A recently developed approach, multiple reaction monitoring (MRM)-profiling, searches for metabolites with precursor (Prec) and neutral loss (NL) scans in a representative sample and creates a list of ion transitions. These are then used in an MRM method for fast screening of individual samples and discrimination between healthy and diseased. A large variety of functional groups are considered and all signals discovered are recorded in the individual samples, making this a largely unsupervised method. MRM-profiling is described here and then demonstrated with data for over 900 human plasma coronary artery disease (CAD) samples. Representative pooled samples for each condition were interrogated using a library of over a hundred Prec and NL scans on a triple quadrupole MS. The data from the Prec and NL experiments were converted into ion transitions, initially some 1266 transitions. Each ion transition was examined in the individual samples on a time scale of milliseconds per transition, which allows for rapid screening of large sample sets (<5 days for 1000 samples). Use of univariate and multivariate statistics allowed classification of the sample set with high accuracy. The metabolite profiles classified the CAD female, CAD male, and peripheral artery disease (PAD) samples relative to controls with an accuracy of 90%, 78%, and 85%, respectively. The compounds responsible for informative ion transitions were identified by chromatography and high resolution MS; some have been previously reported and found to be associated with coronary artery disease metabolism, indicating that the methodology generates a meaningful metabolite profile while being faster than traditional methodologies.