Bacground noise changes

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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Im currently trying to run a calibration of an aqueous peptide sample on our Waters triple quad lc-ms, but I'm finding that when I run the same sample in duplicate, the background noise is changing a lot between runs and so the peak area is drastically changing too. Does anyone have any ideas why this may be? My run has fairly long wash/equilibrate steps built in.

What you are describing could be described more simply as poor reproducibility.
The reasons are many, and here are several to consider: Inadequate column washing (e.g. not using a solvent system which is STRONGER than the mobile phase to wash the column off in between each analysis); too short of an equilibration period (do not start the next run until the baseline is flat and stable); injecting samples which are not fully dissolved into the mobile phase; contaminated flow path (instrument or column); A poor quality method; lack of proper MS tune for the sample types.

After ruling out all of the above items... have you removed the column (place a calibrated restrictor capillay in its place) and run the method to check if the column is contributing the problem? What about maintenance of the HPLC and MS system? Are you sure the systems are clean and meet qualification specs? Have you run true blank samples to check the baseline stability during the run? IOW: Inject mobile phase and also try a dummy injection too (no sample in the needle, but the A/I still switches the valve). Basic troubleshooting steps should be taken.
2 posts Page 1 of 1

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