Of course different systems with different conditions will produce different retention times, that's why most LC/MS providers offer various kinds of tuning mixtures. Have you benchmarked your column with one of those?

If the retention times in your own column are not stable over several samples, you may have oversaturated your column, then everything gets unstable.

Hello Aishwarya,

I would not try to compare the retention time values. They may strongly vary even when using the same instrument and method like in the literature reference, for example due to different dwell volumes when using gradient elution (usually not reported in literature). Elution order is more robust but may also vary with different brands of RP18 columns, different temperatures, or solvent systems.

The mass spectra can also vary to some degree (see reference spectra in mzcloud and massbank) in their proportions of adduct ions, fragments, and coulomb oligomers (such as [2M-H]-). In addition, the mass spectrum may be more or less overlayed with background signals or signals of neighbouring chromatographic peaks, so that your analyte's signals are hardly visible in the spectrum.

Hello, retention time depend from dead volume of system which variates depends from equipment type and tubes connection ways.

Yes retention time and mass spectrum values change as samples to be analysed change because of change in polarity of sample and fragments that make up the sample/ compound or molecule