I am currently looking at different HPLC systems to be used in a 'biomolecule'environment. I am leaning towards the newest Agilent system, whcih is a system I have used extensively in small molecule chromatography. Has anybody had any major problems with the Agilent HPLC when analyzing biomolecules? Are other HPLC systems a cut above the Agilent HPLC?

Since you say you a working with protiens, this most likly means acetonitrile/TFA gradients at low UV wavelengths. Because Agilent 1100 binary systems suffer from mixing problems, you will see significant baseline ripple using these systems and this mobil phase combination. This could cause you problems if you are interested in low levels and will also lead to some RT variation (again due to poor mixing). You can overcome some of these problems by adding a large volume pre-column mixer. This, of course, increases the volume of your system and still does not totally solve your baseline ripple.

Good Luck

I am an Agilent employee. I did an extensive study of the factors that affect the "TFA Mixing" problem back in 1995. It is published in: J. Chrom.(A), 699 (1995) 11-20. The things that are most important are: Column choice, mixing volume, and TFA concentration, in that order. I can FAX you a copy, if you cannot get one of your own. Call me at 800-227-9770 ( option 4) and ask for me.

To Cliff Woodward
I am having problems with baseline shifts, how do suggest this is down to mixing problems if it has been through a column? I am not using ACN/THF, and the detector uses a blue laser. Is this problem due to pressure changes?
Hope you can shed some light (any colour/color would do!)on this subject.
Cheers
Bryan Wallwork

TFA adsorbs on the column, and the column amplifies the mixing problem that you have had in the gradient generator. We had seen this issue in the low UV.
In order to shed more (blue?) light on the problem, we would need to know how blue your laser is....

415nm: nearly a purple haze!
I do not use TFA, in fact none of the mobile phase components absorb at this wavelength, and it is not due to refractive index changes. If a binary mixture has been through an HPLC column, how can it not be mixed???
maybe not so blue, Uwe.
Cheers
Bryan
to answer the initial question, the Waters Alliance system did not suffer from the wavy baseline, but HP and TSP systems did!!

Since you are not using TFA and this is not the right wavelength for the TFA problem, we might safely exclude TFA as the source of your problem. Well at least tentatively....
What other stuff is in your mobile phase besides acetonitrile and water? What is your detection scheme? Absorbance, fluorescene? Waht are you biomolecules? Proteins, peptides, DNA, RNA?

I'm going to quantify protein by using HPLC.May i know what is the best situations of the HPLC like the type of detector,column,mobile phase and the flow rate suit to do yhe work?