biostudies-literaturePino LNIA NIH HHSBelgian American Educational FoundationFonds Wetenschappelijk OnderzoekNational Institute on Aging3936-3943https://www.ebi.ac.uk/biostudies/studies/S-EPMC6824964biostudies-literatureUnknown18(11)For the 2018 YPIC Challenge, contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in <i>Escherichia coli</i>. In addition to deciphering the sentence, contestants were asked to determine the three-dimensional structure and detect any post-translation modifications left by the host organism. We present our experimental and computational strategy to characterize this sample by identifying the unknown protein sequence and detecting the presence of post-translational modifications. The sample was acquired with dynamic exclusion disabled to increase the signal-to-noise ratio of the measured molecules, after which spectral clustering was used to generate high-quality consensus spectra. De novo spectrum identification was used to deterJournal of proteome research2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample.PMC6824964F31 AG055257Lin APino LBittremieux Wfalse2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample.For the 2018 YPIC Challenge, contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in <i>Escherichia coli</i>. In addition to deciphering the sentence, contestants were asked to determine the three-dimensional structure and detect any post-translation modifications left by the host organism. We present our experimental and computational strategy to characterize this sample by identifying the unknown protein sequence and detecting the presence of post-translational modifications. The sample was acquired with dynamic exclusion disabled to increase the signal-to-noise ratio of the measured molecules, after which spectral clustering was used to generate high-quality consensus spectra. De novo spectrum identification was used to deter2019-01-01T00:00:00Z2019 Nov2026-04-16T11:10:23.706Z2019-11-09T08:01:51ZS-EPMC68249643155662010.1021/acs.jproteome.9b00384