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. Author manuscript; available in PMC: 2023 Jul 13.
Published in final edited form as: Nat Protoc. 2022 Nov 16;18(2):396–423. doi: 10.1038/s41596-022-00766-8

Extended Data Fig. 3. Effect of Illumina sequencing cluster density on PepSeq demultiplexed read yield.

Extended Data Fig. 3

The relationship between flowcell cluster density (x-axis) and the total number of reads successfully demultiplexed to peptides and samples (y-axis) across a series of representative sequencing runs by using mid-output (blue dots) or high-output (red dots) 150-cycle Illumina NextSeq kits. We observe a cluster density between 250 and 325 (green shaded region) to yield the greatest number of usable PepSeq reads per run, which substantially exceeds the cluster density recommended by Illumina (blue shaded region). Cluster densities for high-output kits have been normalized by a factor of 3 to allow accurate comparison with mid-output kits.