Fig. 2: Tuning coverage and signal to noise by FAIMS.
a–g, Two hundred and fifty picograms of HeLa cell peptides from diluted bulk digests were injected. Peptides were separated at a throughput of 50 SPD; n = 3 technical replicates. Data were recorded with or without the FAIMS Pro interface unit attached and at the given compensation voltage. Circles in a indicate identified PGs or precursors at a 1% FDR in individual replicates, bars indicate their means, and error bars indicate standard deviations. Dots in b indicate the median CV at the protein level when performing quantification at the MS1 or MS2 level using Spectronaut 18 (DirectDIA+). Dots in c indicate the median number of data points recorded per precursor when performing at the MS1 or MS2 level as indicated (DirectDIA+). The log2 abundance ranks and their density plots for PGs (d) and precursors (e) are shown. The Venn diagrams show the number of PGs (f) or peptides (g) quantified in one representative replicate each using either no FAIMS or FAIMS with a compensation voltage of –48 V or –58 V.
