Direct and automatic chromatography-mass spectral analysis

A method for the analysis of compounds of interest through separation over time when using a mass spectral detection system, comprising the steps of

• a. acquiring, at a plurality of times, mass spectral data throughout a range of mass to charge ratio for ionized particles of a sample;
• b. selecting a relevant retention time window for presence of possible compounds of interest;
• c. using the acquired mass spectral data in said relevant retention time window to perform a mass spectral library search for compounds in a mass spectral library and identify possible compounds along with their retention index values;
• d. performing a regression analysis, using a regression model, between the retention index values of said possible compounds and their retention times by using a subset of compounds identified;
• e. using said regression model to calculate a retention index value based on the measured retention time for a compound;
• and
• f. using said calculated retention index value for one of comparing to previously measured retention index value of a known candidate compound to evaluate the likelihood of its correct identification and comparing to predicted retention index value of a previously unknown compound to evaluate the likelihood of a given possible structure.