Hi,What is your injection solvent and do you get same issue when injecting the reagent blank ? Perform a system performance test by injecting a GC amenable compound (say butane for ex.) to identify problem if it is originating from instrument/consumables or analysis conditions and method parameters/sample properties
does the negative peak appear at the retention time corresponding to the dead volume of the column? if so, it could be a disturbance of the linear velocity of the carrier gas due to the injected volume...
It could be a gas tighy syringe problem. Introducing a small amount of air may flactuate the baseline. This could be due to improper injection or altered syringe. At this point I strongly suggest to inject a liquid sample by using ALS (as preferred) or manually. It may indicate the source of error. Random negative peaks at varying retention times may be seen owing to connection problem and technical service is needed. In that case the peaks are monitored as electronic spikes which consist of max. 2 to 3 data points. Track the backpressure rates during the analysis note if any unusual apparent decrease or increase is occured. If possible clean or change the FID jet, connection and always use gas traps for mobile phase flow. On the other hand, It would be nice to share a chromatogram to identify the problem properly.