%0 Journal Article %J J Proteome Res %D 2019 %T A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry %A Swearingen, Kristian E %A Eng, Jimmy K %A Shteynberg, David %A Vigdorovich, Vladimir %A Springer, Timothy A. %A Mendoza, Luis %A Sather, Noah D %A Deutsch, Eric W %A Kappe, Stefan H I %A Moritz, Robert L %X Thrombospondin type 1 repeats (TSRs), small adhesive protein domains with a wide range of functions, are usually modified with O-linked fucose, which may be extended to O-fucose-β1,3-glucose. Collision-induced dissociation (CID) spectra of O-fucosylated peptides cannot be sequenced by standard tandem mass spectrometry (MS/MS) sequence database search engines because O-linked glycans are highly labile in the gas phase and are effectively absent from the CID peptide fragment spectra, resulting in a large mass error. Electron transfer dissociation (ETD) preserves O-linked glycans on peptide fragments, but only a subset of tryptic peptides with low m/ z can be reliably sequenced from ETD spectra compared to CID. Accordingly, studies to date that have used MS to identify O-fucosylated TSRs have required manual interpretation of CID mass spectra even when ETD was also employed. In order to facilitate high-throughput, automatic identification of O-fucosylated peptides from CID spectra, we re-engineered the MS/MS sequence database search engine Comet and the MS data analysis suite Trans-Proteomic Pipeline to enable automated sequencing of peptides exhibiting the neutral losses characteristic of labile O-linked glycans. We used our approach to reanalyze published proteomics data from Plasmodium parasites and identified multiple glycoforms of TSR-containing proteins. %B J Proteome Res %V 18 %P 652-663 %8 2019 Feb 01 %G eng %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/30523691?dopt=Abstract %R 10.1021/acs.jproteome.8b00638