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. 2019 Sep 20;15(9):e8994. doi: 10.15252/msb.20198994

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© 2019 The Authors. Published under the terms of the CC BY 4.0 license

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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xiSEARCH is an open source search engine that takes a peak list as input. Users can define any type of crosslinker, modification, digestion and fragmentation method. The output is a list of matches in .csv format. We use xiFDR to filter results to the desired confidence level.

xiSEARCH + xiFDR(Xi), pLink 2 and Kojak(+PeptideProphet) comparison at 5% residue‐pair FDR. The same trypsin dataset of the 26S proteasome was searched with all three software packages. xiSEARCH was run twice—once giving same likelihood for matching lysine, serine, threonine and tyrosine (xiSEARCH), as is the case for Kojak and pLink 2, and once giving priority to Lysine (Xi*).