Extended Data Fig. 2: Examples of variant peptide–spectrum matches from the analysis of healthy donor stem cells.
From: ProHap enables human proteomic database generation accounting for population diversity
Amino acid substitutions in sequences are marked in bold, posterior error probabilities are estimated by Percolator43. The top part of each plot shows the spectrum measured from the sample, with the blue peaks highlighting ions that match the theoretical spectrum. The bottom part of each plot shows the fragmentation and intensities predicted by MS2PIP37, with the green peak highlighting matched predictions, and the red peaks showing predictions that do not have a corresponding peak in the observed spectrum. A: Two peptide–spectrum matches covering the reference and alternative allele for a variant (rs1132979). Please follow these links to view the annotated spectra using the Universal Spectrum Identifier: Spectrum 1 (https://massive.ucsd.edu/ProteoSAFe/usi.jsp#%7B%22usi%22%3A%22mzspec%3APXD053601%3A20230601_ASC2_NEO3_X866_P244_R771_180min_uPAC110cm_27ms_DDA_S3.mzML%3Ascan%3A96472%3ANTVLATWQPYTTSK%2F2%22%7D), Spectrum 2 (https://massive.ucsd.edu/ProteoSAFe/usi.jsp#%7B%22usi%22%3A%22mzspec%3APXD053601%3A20230601_ASC2_NEO3_X866_P244_R771_180min_uPAC110cm_27ms_DDA_S3.mzML%3Ascan%3A92494%3ANTVLATWQPYSTSK%2F2%22%7D) B: Two multi-variant peptide–spectrum matches, covering the alternative allele for multiple variants co-occurring in the same haplotype of the donor. Please follow these links to view the annotated spectra using the Universal Spectrum Identifier: Spectrum 3 (https://massive.ucsd.edu/ProteoSAFe/usi.jsp#%7B%22usi%22%3A%22mzspec%3APXD053601%3A20230601_ASC2_NEO3_X866_P244_R771_180min_uPAC110cm_27ms_DDA_S2.mzML%3Ascan%3A107817%3AELSGLPSGPSAGSGPPPPPPGPPPPPVSTSSGSDESASR%2F3%22%7D), Spectrum 4 (https://massive.ucsd.edu/ProteoSAFe/usi.jsp#%7B%22usi%22%3A%22mzspec%3APXD053601%3A20230601_ASC2_NEO3_X866_P244_R771_180min_uPAC110cm_27ms_DDA_S2.mzML%3Ascan%3A147106%3ALLGLELSEAEALGADSAR%2F2%22%7D).
