Samples were analyzed using an Ultimate 3000 liquid chromatograph coupled with a Q-Exactive mass spectrometer (Thermo Scientific) and positive electrospray ionization. Mobile phases were 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile. We used an Agilent SB-C18 RRHD 1.8 µm, 2.1 x 150 mm column and a 55-minute method with a gradient of 5% B to 95%B. Calibration points, blanks, and daily, weekly, and 5-week composite samples were analyzed using an alternating full MS and all ion fragmentation (AIF) method. Additionally, the 5-week composite samples were analyzed using data dependent MS2 (ddMS2) analysis with an iterative inclusion approach, which has similar advantages to previously reported intelligent acquisition methods . Briefly, we used the full scan data to generate inclusion lists including all features after blank filtering to ensure ddMS2 spectra were collected for each peak in the three 5-week composite samples. Each 5-week composite was injected 10 or 11 times, each run with a separate inclusion list for ddMS2 data collection. Additional instrument method and iterative inclusion information is in sections S.1.2-3 and S.2.3.