Fig. 2: Influence of protein database size on the non-cleavable search of MS Annika. | Communications Chemistry

Fig. 2: Influence of protein database size on the non-cleavable search of MS Annika.

From: Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex

Fig. 2

Mass spectrometry data of C. elegans nuclei was searched with MS Annika once using the full C. Elegans proteome (n = 26 695) and once using a filtered proteome of abundant proteins identified in a linear search (n = 3266). Results were validated for 1% estimated FDR with xiFDR24. Interestingly, the number of identified crosslinks does not show large variation, regardless of database size with the biggest difference observed in replicate one where the filtered database search reports 45 more crosslinks. Overall 476 unique crosslinks are identified across the three replicates using the filtered proteome and 435 unique crosslinks using the full proteome which shows the applicability of MS Annika for large proteome-wide studies.

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