Figure 2.

Identification and quantification errors: (A) Schematic of the experiment where M. musculus BMDMs and C. albicans were lysed separately for proteomics, and subsequently C. albicans lysates were spiked with the BMDM lysates (M. musculusn = 3, C. albicansn = 1). The number of (B) M. musculus peptides and (C) M. musculus proteins, identified using either a M. musculus-only (M) or M. musculus and C. albicans (M+C) FASTA. Proteins identified from only one peptide are highlighted in white. The number of (D) C. albicans peptides and (E) C. albicans proteins identified using the M. musculus and C. albicans (M+C) FASTA. Volcano plots showing the Log₂ fold change of the spiked versus the nonspiked samples and the -Log₁₀(p-value) for (F) Spectronaut 16 (S16) using default identification settings and a M. musculus-only FASTA and (G) Spectronaut 16 (S16) using default identification settings and a M. musculus and a C. albicans FASTA. Proteins with a q-value <0.05 and a log₂ fold change >2 or <-2 are highlighted, as shown in the key.