Step 2: Compound Matching. For each target m/z value, compounds from the reference library are selected as potential matches. In the preliminary implementation of the ILSA, we generated the list of reference m/z values to match against by considering either the (i) calculated protonated molecule m/z of all library compounds, or (ii) observed base peak m/z from the low-fragmentation is-CID library spectrum of all library compounds; but not both simultaneously. The library entries with reference m/z values that fell within a user prescribed mass tolerance of the target m/z (e.g., ±0.005 Da) were considered potential matches and proceeded to step 3 for scoring. From Step 3. Compute classification scores (Θ) between library entries and sample spectra using all acquired is-CID mass spectra. experimentation, we observed that target m/z values from the mixture were occasionally not identified as a protonated molecule or base peak but could be explained as either the major isotope of one of these peaks or as a major fragment ion from the library compound that was not the base peak. Accordingly, we now generate the list of reference m/z values to include (i) protonated molecule, (ii) low fragmentation spectrum base peak, (iii) prominent isotope (most abundant between M+1 or M+2) of the protonated molecule, (iv) prominent isotope of the base peak, and (v) second highest intensity ion with relative intensity at least 5 % (referred to as the major fragment ion, if present)-all reference m/z values are calculated during the library building process and all target-types are identified simultaneously. Note that for many compounds, the protonated molecule and low fragmentation spectrum base peak are the same. This larger reference m/z list can provide a broader set of potential matches for every target m/z and explain more peaks in the mixture, and does not add appreciable computing time with the library sizes thus far considered.