<<< Full experiment listing

PXD000292

PXD000292 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleChaFRADIC: A novel SCX-based approach for N-terminal Enrichment
DescriptionStep 1: Cell lysis of yeast sphaeroblast (Saccharomyces cerevisiae) and carbamidomethylation. Step 2: Isotopic labeling with dimethylation (light + medium). Step 3: Proteolytic digestion with trypsin (ArgC specificity because of blocked lysines by dimethylation). Step 4: Enrichment via ChaFRADIC method Step 5: Nano-LC-MS/MS measurements Step 6: Data interpretation. Specifications: --ESI spray ionisation o Q Exactive mass spec. --Quadrupole selection, HCD fragmentation and orbitrap detection o Identification + Quantification: PD version 1.3.0039. Search engine: Mascot 2.4. SGD database (Sep 2011), 6717 target sequences. Special nodes: precursor ions quantifier (within a 1 min retention time window), percolator (default settings). Protease: SemiArgC with max. 2 missed cleavage sites. Used modifications: Yeast_N-term_Enriched_Search_Acetylation Variable --  N-terminal Acetylation (42.0105 Da) --  Dimethylation light (28.0313 Da) at Lys --  Dimethylation medium (34.0689 Da) at Lys fixed --  Carbamidomethylation at Cys (57.0214 Da) Quantification --  Peptides with labeled lysine Yeast_N-term_Enriched_Search_Dimethylation Variable --  N-terminal Dimethylation light (28.0313 Da) --  N-terminal Dimethylation medium (34.0689 Da) --  Dimethylation light (28.0313 Da) at Lys --  Dimethylation medium (34.0689 Da) at Lys fixed --  Carbamidomethylation at Cys (57.0214 Da) Quantification --  Peptides with labeled N-terminus --  Peptides with labeled N-terminus and labeled lysine. Mass tolerance: 10 ppm for MS, 0.02 Da for MS/MS. Applied filters: high confidence (FDR <1%), search engine rank 1
HostingRepositoryPRIDE
AnnounceDate2014-07-25
AnnouncementXMLSubmission_2014-07-25_01:16:13.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSaskia Venne
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListacetylated residue; iodoacetamide derivatized residue; deuterated dimethyl labeling (D); dimethylated residue; alpha-amino dimethylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-06-20 02:21:44ID requested
12013-08-09 07:56:40announced
12013-12-13 07:04:47announced
22014-07-25 01:16:13announcedUpdated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: ChaFRADIC, degradomics, N-terminal, COFRADIC, Icp55, protease, peptidase, yeast
Contact List
Saskia Venne
contact affiliationBioanalytik
contact emailsaskia.venne@isas.de
dataset submitter
Full Dataset Link List
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/2013/08/PXD000292
PRIDE project URI
Repository Record List
[ + ]