2014, McFarland, B.K., Berrah, N., Bostedt, C., Bozek, J., Bucksbaum, P.H., Castagna, J.C., Coffee, R.N., Cryan, J.P., Fang, L., Farrell, J.P., Feifel, R., Gaffney, K.J., Glownia, J.M., Martinez, T.J., Miyabe, S., Mucke, M., Murphy, B., Natan, A., Osipov, T., Petrovic, V.S., Schorb, S., Schultz, T., Spector, L.S., Swiggers, M., Tarantelli, F., Tenney, I., Wang, S., White, J.L., White, W., Gühr, M.

Free electron laser (FEL) based x-ray sources show great promise for use in ultrafast molecular studies due to the short pulse durations and site/element sensitivity in this spectral range. However, the self amplified spontaneous emission (SASE) process mostly used in FELs is intrinsically noisy resulting in highly fluctuating beam parameters. Additionally timing synchronization of optical and FEL sources adds delay jitter in pump-probe experiments. We show how we mitigate the effects of source noise for the case of ultrafast molecular spectroscopy of the nucleobase thymine. Using binning and resorting techniques allows us to increase time and spectral resolution. In addition, choosing observables independent of noisy beam parameters enhances the signal fidelity.