In a comprehensive two-dimensional gas chromatograph, a thermal modula
tor serially couples two columns containing dissimilar stationary phas
es. The secondary column generates a series of high-speed secondary ch
romatograms from the sample stream formed by the chromatogram eluting
from the primary column, This series of secondary chromatograms forms
a two-dimensional gas chromatogram with peaks dispersed over a retenti
on plane rather than along a line. The method is comprehensive because
the entire primary column chromatogram is transmitted through the sec
ondary column with fidelity. One might expect that a two-dimensional s
eparation in which both dimensions are basically the same technique, g
as chromatography, would be inefficient because the two dimensions wou
ld behave similarly, generating peaks whose retentions correlate acros
s dimensions. Applying a temperature program to the two columns, howev
er, can tune the separation to eliminate this inefficiency. The temper
ature program reduces the retentive power of the secondary column as a
function of progress of the primary chromatogram such that the retent
ion mechanism of the primary column is eliminated from the second dime
nsion. Retention of a substance in the second dimension is then determ
ined by the difference in its interaction with the two stationary phas
es, Retention times in the second dimension then fall within a fixed r
ange, and the whole retention plane is accessible, In a properly tuned
comprehensive two-dimensional chromatogram, retention times in the tw
o dimensions are independent of each other, and the two-dimensional ch
romatogram is orthogonal. Orthogonality is important for two reasons.
First, an orthogonal separation efficiently uses the separation space
and so has either greater speed or peak capacity than nonorthogonal se
parations. Second, retention in the two dimensions of an orthogonal ch
romatogram is determined by two different and independent mechanisms a
nd so provides two independent measures of molecular properties.