PXD000380

PXD000380 is an original dataset announced via ProteomeXchange.

Title	KMH2 control treatment
Description	We investigate molecular effects of glucosamine supplements, a popular safe alternative to non-steroidal anti-inflamatory drugs for decreasing pain, inflammation and keeping joints healthy. Numerous publications state an array of different molecular effects upon glucosamine treatment. We question whether these differences resulted mainly from focusing on a specific sub proteome or because different cell lines or tissues were used in the previous studies. To address this question global MS- and transcription array-based glucosamine drug profiling were performed on lymphocyte derived cell lines. We combined global label free MS-based protein quantitation with an open search strategy to obtain the best possible proteome coverage. Our result in large part support previous findings in a variety of cell models. Glucosamine induce O-GlcNAcylation but we also observe global changes in acetylation, methylation, phosphorylation. Furthermore, we mapped novel O-GlcNAc sites, on ER lumen proteins, regulated upon glucosamine treatment which provides novel insights into the role of glucosamine in ER stress. Preprocessing of MS data: All Q-Exactive data were calibrated using polycyclodi-methylsiloxane (PCMs—outgassed material from semiconductors) present in the ambient air and Bis(2-Ethylhexyl)(Phthalate) (DEHP—from plastic)1, 2 using both MaxQuant version 1.3.0.53 and modular VEMS mVEMS4. mVEMS4 further allows alternative parent ion annotations for each MS/MS spectrum which is needed if two peptide elution profiles overlap in the m/z and retention time dimension. By allowing alternative parent ion annotation for each MS/MS spectrum, provides a space efficient data format. Furthermore these alternative parent ion annotations were taken into account during the search. Database dependent search of MS data: All data were searched with MaxQuant version 1.3.0.53 and VEMS5. Mass accuracy was set to 10 ppm for peptides and 10 mDa for peptide fragments. Four missed cleavages were specified and the database UniProtKB/TrEMBL were used including permutated protein sequences, leaving Lys and Arg in place, together with common contaminants such as human keratins, bovine serum proteins and proteases6. Fixed modification of carbamidomethyl cysteine was included in the search parameters. In MaxQuant the following variable modifications were considered: Met-loss (UNIMOD 765), Oxidized methionine (UNIMOD 885), O-GlcNAc (HexNAc, UNIMOD 43). In VEMS a list of variable 36 modifications were considered for all data against the full protein database were performed. Protein N-terminal Met-loss is not in the list of VEMS modifications since VEMS by default always looks for N-terminal Met-loss. The modifications Phosphate-ribosylation (UNIMOD 1356), ADP ribose (UNIMOD 213), hydroxylation (UNIMOD 35) and Myristoylation (UNIMOD 45) were not frequent at a 1% FDR threshold and the search was therefore repeated excluding these modifications.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_02:43:27.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rune Matthiesen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue; carbamoylated residue; monomethylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-30 01:18:16	ID requested
1	2014-08-20 02:48:25	announced
⏵ 2	2014-10-23 02:43:28	announced	Updated project metadata.

Carvalho AS, Ribeiro H, Voabil P, Penque D, Jensen ON, Molina H, Matthiesen R, Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress. Mol Cell Proteomics, 13(12):3294-307(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: KMH2 PTMs drug profilling

Rune Matthiesen
contact affiliation	Population genetics
contact email	rmatthiesen@ipatimup.pt
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/2014/08/PXD000380

PRIDE project URI

• PRIDE
  1. PXD000380
     1. Label: PRIDE project
     2. Name: KMH2 control treatment