A process for isolating and simultaneously amplifying a first and a second target nucleic acid that may be present in one or more fluid samples, said process comprising the automated steps of: a. adding a quantitative standard nucleic acid to each of said fluid samples, wherein the sequence of the quantitative standard nucleic acid is derived from a source different from the origin of the fluid samples, is different from the other nucleic acid sequences in the fluid samples, is derived from a plant genome and is scrambled, wherein said quantitative standard nucleic acid has a concentration between 20xLOD and 5000xLOD b. combining together a solid support material and said one or more fluid samples in one or more vessels for a period of time and under conditions sufficient to permit nucleic acids comprising the target nucleic acids and the quantitative standard nucleic acid to be immobilized on the solid support material c. isolating the solid support material from the other material present in the fluid samples in a separation station d. purifying the nucleic acids in said separation station and washing the solid support material one or more times with a wash buffer e. contacting the purified target nucleic acids and the purified quantitative standard nucleic acid with amplification reagents comprising at least one distinct set of primers for each of said target nucleic acids and for said quantitative standard nucleic acid in at least two reaction vessels for amplification of the at least first and second target nucleic acids and the quantitative standard nucleic acid in the at least two reaction vessels f. incubating in said reaction vessels said purified target nucleic acids and said purified quantitative standard nucleic acid with said amplification reagents for a period of time and under conditions sufficient for an amplification reaction indicative of the presence or absence of said target nucleic acids to occur while amplifying the first, but not the second target nucleic acid in the first reaction vessel and the second, but not the first target nucleic acid in the second reaction vessel g. detecting and measuring signals generated by the amplification products of said target nucleic acids and being proportional to the concentration of said target nucleic acids, and detecting and measuring a signal generated by said quantitative standard nucleic acid h. determining the quantity of one or more of said target nucleic acids by using the quantitative standard nucleic acid as a reference wherein the conditions for amplification and detection in steps e. to g. are identical for said first and second purified target nucleic acids and said quantitative standard nucleic acid. a. adding a quantitative standard nucleic acid to each of said fluid samples, wherein the sequence of the quantitative standard nucleic acid is derived from a source different from the origin of the fluid samples, is different from the other nucleic acid sequences in the fluid samples, is derived from a plant genome and is scrambled, wherein said quantitative standard nucleic acid has a concentration between 20xLOD and 5000xLOD b. combining together a solid support material and said one or more fluid samples in one or more vessels for a period of time and under conditions sufficient to permit nucleic acids comprising the target nucleic acids and the quantitative standard nucleic acid to be immobilized on the solid support material c. isolating the solid support material from the other material present in the fluid samples in a separation station d. purifying the nucleic acids in said separation station and washing the solid support material one or more times with a wash buffer e. contacting the purified target nucleic acids and the purified quantitative standard nucleic acid with amplification reagents comprising at least one distinct set of primers for each of said target nucleic acids and for said quantitative standard nucleic acid in at least two reaction vessels for amplification of the at least first and second target nucleic acids and the quantitative standard nucleic acid in the at least two reaction vessels f. incubating in said reaction vessels said purified target nucleic acids and said purified quantitative standard nucleic acid with said amplification reagents for a period of time and under conditions sufficient for an amplification reaction indicative of the presence or absence of said target nucleic acids to occur while amplifying the first, but not the second target nucleic acid in the first reaction vessel and the second, but not the first target nucleic acid in the second reaction vessel g. detecting and measuring signals generated by the amplification products of said target nucleic acids and being proportional to the concentration of said target nucleic acids, and detecting and measuring a signal generated by said quantitative standard nucleic acid h. determining the quantity of one or more of said target nucleic acids by using the quantitative standard nucleic acid as a reference