The noise depends on several parameters in HPLC-MS (e.g. mobile phase type, solvent brand, column, whether a maintenance was just performed on the HPLC, source parameter values etc.), but it is notoriously high on single and triple quadrupoles in full scan mode. By increasing the scan time you have flattened the trace and decreased the noise but, as we can see in the chromatograms you posted, the s/n ratio for your peak at 1.7 min hasn't changed. I am not saying it was a bad idea to increase the scan time, it was actually very appropriate in your case (1000 Da/s is the fastest rate modern quads can efficiently deal with, and lower rates would always be preferable) but it had no effect on s/n ratios. To improve signal-to-noise ratios, and assuming that your HPLC and mobile phases are reasonably clean (meaning there is nothing abnormal with your instrument - you can ask your Shimadzu contact about it, they must have hundreds of examples in-house) you can display the BPI chromatogram instead of the TIC, which should improve things a bit. Another option would be to check which ions are the highest (usually small ions between 50-150 Da) and, if possible, start the scan at a higher mass. Otherwise increase the amounts injected, if possible.