HUMAN PROTEINPEDIA 


Experimental Details - HuPA_00671
Experiment type Mass spectrometry
Short description Proteomic characterization of human embryonic stem cell differentiation into oligodendrocytes
Experimental description Two sets of LC-MS/MS analyses of iTRAQ labeled peptides were carried out using four key stages of oligodendrocyte differentiation from human ESCs, including the ES stage, neural precursor (NP) stage, glial precursor (GP) stage, and the OP stage.. Samples analyzed on LTQ-Orbitrap XL generated a total of ~100,000 spectral search inputs using Proteome Discoverer spectrum selector software. Similarly, samples analyzed on LTQ-Orbitrap Velos resulted in ~103,000 spectral search inputs. Using stringent false discovery cutoff of 0.01, ~9,400 unique peptides (1,643 unique proteins) were identified from LTQ-Orbitrap XL and ~17,200 unique peptides (2,378 unique proteins) were identified from LTQ-Orbitrap Velos. By combining the search results from both experiments and Mascot and Sequest search resulted in the identification and quantitation of 3,024 unique proteins at a false discovery rate cutoff of 0.01. In addition to generating a comprehensive proteomics database of OP differentiation, the data set helped to characterize the progressive stage-specific expression of proteins with known or suspected roles in myelination and to identify novel markers of NPs, GPs, and OPs, utilizing a human ESC model of oligodendrocyte differentiation.
Principal Investigator's NameDr. Akhilesh Pandey
TitleProfessor
E-mailpandey@jhmi.edu
AddressJohns Hopkins University
733, N. Broadway, BRB560
Baltimore, Maryland 21205
CountryUSA
Lab URLhttp://pandeylab.igm.jhmi.edu/
Data submitted byRaghothama Chaerkady
TitlePh.D.
E-mailraghothama@jhmi.edu
Published/Unpublished Unpublished
Journal name Not applicable
PubMed ID Not applicable
Sample source
Tissue:
Cell line: Human embryonic stem cells (H1 Wi cell)
Source organism Homo sapiens [Taxonomy:9606]
Labeling technique 4plex iTRAQ
Protease used Trypsin
Is the sample from in gel No
Reduction and Alkylation Yes
Mass spectrometer
Instrument: LTQ-Orbitrap XL & LTQ-Orbitrap Velos
Vendor: ABI/SCIEX
Ionization method ESI [PSI:1000073]
Fragmentation method HCD
Mass tolerance used for database searching (MS) 20 PPM
Mass tolerance used for database searching (MS/MS) 0.1 Da
Database used for searching RefSeq Release 40 - Human
Search engine used Mascot & Sequest
Download MS raw dataset  
Download processed files  



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