Experimental Details - HuPA_00702
Experiment type Mass spectrometry
Short description Quantitative proteomic profiling of rheumatoid arthritis and osteoarthritis synovial fluid
Experimental description Synovial fluid samples from osteoarthritis (OA) and rheumatoid arthritis (RA) patients were pooled and subjected to depletion using multiple affinity removal system to remove the abundant proteins. The depleted protein was then trypsin digested and labeled with iTRAQ reagents (OA with 116 and RA with 117). The labeled peptides were then subjected to SCX-based fractionation. All the fractions were analyzed on the high resolution Orbitrap Velos mass spectrometer.
Principal Investigator's NameAkhilesh Pandey
AddressInstitute of Bioinformatics
560 Broadway Research Building 733 N. Broadway
Baltimore, MD 21205
Data submitted byLavanya Balakrishnan
TitlePh.D. Student
Published/Unpublished Unpublished
Journal name Not applicable
PubMed ID Not applicable
Sample source
Tissue: Synovial fluid [eVOC:EV:0100429]
Cell line:
Source organism Homo sapiens [Taxonomy:9606]
Labeling technique iTRAQ (OA with 116 and RA with 117)
Protease used Trypsin
Is the sample from in gel No
Reduction and Alkylation Yes
Mass spectrometer
Instrument: LTQ-Orbitrap Velos
Vendor: Thermo Scientific
Ionization method Nanospray
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 50
Search engine used Sequest and Mascot
Download MS raw dataset  
Download processed files  

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