@article {1404801,
	title = {A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry},
	journal = {J Proteome Res},
	volume = {18},
	number = {2},
	year = {2019},
	month = {2019 Feb 01},
	pages = {652-663},
	abstract = {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.},
	issn = {1535-3907},
	doi = {10.1021/acs.jproteome.8b00638},
	author = {Swearingen, Kristian E and Eng, Jimmy K and Shteynberg, David and Vigdorovich, Vladimir and Springer, Timothy A. and Mendoza, Luis and Sather, Noah D and Deutsch, Eric W and Kappe, Stefan H I and Moritz, Robert L}
}
