PXD011784

PXD011784 is an original dataset announced via ProteomeXchange.

Title	Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry
Description	Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). If 4Hyp is lacking at the Yaa position, then Pro at the Xaa position should remain unmodified. Nevertheless, in literature 16 positions have been described where Hyp occurs at the Xaa position (?xHyp) lacking an adjacent 4Hyp. We report four additional positions in liver and colorectal liver metastasis tissue (CRLM). We studied the sequence commonalities between the 20 known positions of ?xHyp. Alanine and glutamine were frequently present adjacent to ?xHyp. We showed that proline, position 584 in COL1A2, had a lower rate of modification in CRLM than in healthy liver. The isomeric identity of ?xHyp, i.e. 3- and/or 4Hyp, remains unknown. We present a proof of principle identification of ?xHyp. This identification is based on liquid chromatography retention time differences and mass spectrometry using ETD-HCD fragmentation, complemented by ab initio calculations. Both techniques identify ?xHyp at position 584 in COL1A2 as 4-hydroxyproline (4xHyp).
HostingRepository	PRIDE
AnnounceDate	2019-03-20
AnnouncementXML	Submission_2019-04-09_02:04:25.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nick van Huizen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-21 08:00:24	ID requested
1	2019-03-20 09:12:14	announced
⏵ 2	2019-04-09 02:04:27	announced	Updated publication reference for PubMed record(s): 30945869.

van Huizen NA, Burgers PC, Saintmont F, Brocorens P, Gerbaux P, Stingl C, Dekker LJM, IJzermans JNM, Luider TM, Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry. J Proteome Res, 18(5):2045-2051(2019) [pubmed]

submitter keyword: Collagen, hydroxyproline, PTM, posttranslational modification, mass spectrometry, ETD, Orbitrap Fusion, Ab initio, liver, colorectal liver metastasis

Theo M. Luider
contact affiliation	Lab. Neuro-Oncology and Clinical Cancer Proteomics, Erasmus Medical Center, the Netherlands ( lab head )
contact email	t.luider@erasmusmc.nl
lab head
Nick van Huizen
contact affiliation	Erasmus MC
contact email	n.vanhuizen@erasmusmc.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/03/PXD011784

PRIDE project URI

• PRIDE
  1. PXD011784
     1. Label: PRIDE project
     2. Name: Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry