PXD009202

PXD009202 is an original dataset announced via ProteomeXchange.

Title	MudPIT analyses of the protein succination after fumarate treatment of whole cell extracts from Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) fumarate hydratase-deficient (FH-/-) cells
Description	In brief, TCA-precipitated proteins from whole cell extracts treated with fumarate were urea-denatured, reduced, alkylated, and digested with endoproteinase LysC followed by trypsin. The peptide mixtures were loaded onto microcapillary fused silica columns (100um i.d.), packed with C18 reverse phase (Aqua; Phenomenx), SCX (Luna; Phenomenex) and C18-RP, placed in-line with an Agilent 11000 quaternary pump, and analyzed by a 10-step MudPIT on Orbitrap Velos Pro or Elite. Full MS spectra were recorded on the eluting peptides over a 400 to 1600 m/z range in the Orbitrap at 60K resolution, followed by fragmentation in the ion trap (at 35% collision energy) on the first to fifteenth most intense ions selected from the full MS spectrum. MS/MS datasets searched using ProLuCID (Xu et al., 2015) with a peptide mass tolerance of 10 ppm and 500 ppm for fragment ions. Trypsin specificity was imposed on both ends of candidate peptides during the search against a protein database combining 36,628 human proteins (NCBI 2016-06-10 release), as well as 193 usual contaminants such as human keratins, IgGs and proteolytic enzymes. To estimate false discovery rates (FDR), each protein sequence was randomized (keeping the same amino acid composition and length) and the resulting "shuffled" sequences were added to the database, for a total search space of 73,642 amino acid sequences. Masses of 57.0215 Da and 116.0112 Da were differentially added to cysteine residues to account for alkylation by CAM and succination, respectively, while 15.9949 Da were differentially added to methionine residues. Peptide/spectrum matches were sorted and selected using DTASelect with the following criteria set: spectra/peptide matches were retained only if they had a DeltCn of at least 0.8, and minimum XCorr of 1.8 for singly, 2.0 for doubly, and 3.0 for triply charged spectra. Additionally, the peptides had to be minimum 7 amino acids in length and fully tryptic.
HostingRepository	MassIVE
AnnounceDate	2018-11-26
AnnouncementXML	Submission_2018-11-26_08:43:58.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laurence Florens
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine; 2-succinyl
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-13 08:55:47	ID requested
⏵ 1	2018-11-26 08:43:59	announced

no publication

submitter keyword: succination, fumarate, oncometabolite, chemoproteomic

Laurence Florens
contact affiliation	The Stowers Institute for Medical Research
contact email	laf@stowers.org
lab head
Laurence Florens
contact affiliation	Stowers Institute for Medical Research
contact email	laf@stowers.org
dataset submitter

MassIVE dataset URI

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