PXD000073

PXD000073 is an original dataset announced via ProteomeXchange.

Title	Terminal alkynes react with active-site cysteine nucleophiles
Description	Propargyl labeled ubiquitin was immobilized on beads and used for click-chemistry based pull downs. Covalently linked proteins were washed and digested off-bead, or eluted with strong acid and loaded into a SDS-PAGE gel. Digestion with Lys-C, trypsin consequetively and LC-MS/MS. Both dimethyl labeling, as well as qualitative measurements were done. For both the qualitative and the quantitative dataset peak lists were generated from the raw data files using the Proteome Discoverer software package version 1.3.339. Peptide identification was performed by searching the combined peak lists of the entire gel lane (10 bands) against a concatenated target-decoy database containing the human sequences in the Uniprot database (release 2012_06) supplemented with a common contaminants database using the Mascot search engine version 2.3 via the Proteome Discoverer interface. The search parameters included the use of trypsin as proteolytic enzyme allowing up to a maximum of 2 missed cleavages. For the qualitative dataset, carbamidomethylation of cysteines was set as a fixed modification whereas oxidation of methionines was set as variable modification. Precursor mass tolerance was initially set at 50 ppm, while fragment mass tolerance was set at 0.6 Da. Subsequently, the peptide identifications were filtered for true mass accuracy <10 ppm and an ion score of 25. For the quantitative dataset carbamidomethylation of cysteines was set as a fixed modification whereas oxidation of methionines and the dimethyl light and intermediate labels on N-termini and lysine residues were set as variable modifications. Precursor mass tolerance was initially set at 50 ppm, while fragment mass tolerance was set at 0.6 Da for ETD-IT fragmentation and 0.05 Da for HCD and ETD-FT fragmentation. Subsequently, the peptide identifications were filtered for true mass accuracy <10 ppm and an ion score of 25.
HostingRepository	PRIDE
AnnounceDate	2013-08-14
AnnouncementXML	Submission_2013-08-14_06:24:03.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000073
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Patrick Wijten
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; neutral loss: 63.998285; iodoacetamide derivatized residue; formylated residue; dihydroxylated residue
Instrument	radial ejection linear ion trap; radial ejection linear ion trap

Revision	Datetime	Status	ChangeLog Entry
0	2012-11-20 08:33:44	ID requested
1	2013-08-14 06:07:40	announced
1	2014-07-28 00:25:17	announced
⏵ 2	2013-08-14 06:24:03	announced	Add reference

Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, de Jong A, Goerdayal S, Neefjes J, Heck AJ, Komander D, Ovaa H, On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc, 135(8):2867-70(2013) [pubmed]

submitter keyword: Click chemistry, propargyl, deubiquitinating enzymes, ubiquitin, DUB, mouse

Patrick Wijten
contact affiliation	Faculty of Science
contact email	P.wijten@uu.nl
Arjen Scholten
contact attribute	A.Scholten@uu.nl
contact affiliation	Utrecht University
contact email	A.Scholten@uu.nl

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/2013/08/PXD000073

• PRIDE
  1. 27942
     1. InstrumentRef: INSTRUMENT_2
     2. Label: Ub76_UbPrg_ETD-IT_rep2
     3. ModificationList: formylated residue, dihydroxylated residue, iodoacetamide derivatized residue, monohydroxylated residue,
     4. Name: Indepth qualitative screen Ub76(light) vs UbPrg(intermediate) dimethyl ETD-IT Replicate 2
     5. PublicationRef: PMID23387960
  2. 27940
     1. InstrumentRef: INSTRUMENT_2
     2. Label: Ub76_UbPrg_HCD_rep1
     3. ModificationList: formylated residue, dihydroxylated residue, monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
     4. Name: Indepth qualitative screen Ub76(light) vs UbPrg(intermediate) dimethyl HCD Replicate 1
     5. PublicationRef: PMID23387960
  3. 27939
     1. InstrumentRef: INSTRUMENT_2
     2. Label: Ub76_UbPrg_ETD-IT_rep1
     3. ModificationList: formylated residue, dihydroxylated residue, iodoacetamide derivatized residue, monohydroxylated residue,
     4. Name: Indepth qualitative screen Ub76(light) vs UbPrg(intermediate) dimethyl ETD-IT Replicate 1
     5. PublicationRef: PMID23387960
  4. 27937
     1. InstrumentRef: INSTRUMENT_1
     2. Label: UbPrg_qualitative
     3. ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
     4. Name: Indepth qualitative screen UbPrg pulldown of EL4 cells
     5. PublicationRef: PMID23387960
  5. 27941
     1. InstrumentRef: INSTRUMENT_2
     2. Label: Ub76_UbPrg_ETD-FT_rep2
     3. ModificationList: formylated residue, dihydroxylated residue, iodoacetamide derivatized residue,
     4. Name: Indepth qualitative screen Ub76(light) vs UbPrg(intermediate) dimethyl ETD-FT Replicate 2
     5. PublicationRef: PMID23387960
  6. 27938
     1. InstrumentRef: INSTRUMENT_2
     2. Label: Ub76_UbPrg_ETD-FT_rep1
     3. ModificationList: formylated residue, dihydroxylated residue, monohydroxylated residue, iodoacetamide derivatized residue,
     4. Name: Indepth qualitative screen Ub76(light) vs UbPrg(intermediate) dimethyl ETD-FT Replicate 1
     5. PublicationRef: PMID23387960
  7. 27943
     1. InstrumentRef: INSTRUMENT_2
     2. Label: Ub76_UbPrg_HCD_rep2
     3. ModificationList: formylated residue, dihydroxylated residue, monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
     4. Name: Indepth qualitative screen Ub76(light) vs UbPrg(intermediate) dimethyl HCD Replicate 2
     5. PublicationRef: PMID23387960