Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-2.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-3.dat-pride.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-36B-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-36A-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-38B-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-38A-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-38A-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-38B-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-40B-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-41A-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-36B-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-39B-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-39A-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-41A-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-41B-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-41B-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-39B-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-36A-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-39A-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-40A-2.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-40B-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-40A-2.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-3.wiff.scanftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-3.wiffftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-41B-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38B - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38B - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-38B-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-41A-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-40A-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39B - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38A - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-39B-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40B - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39A - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36B - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38A - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41B - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40A - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41A - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-36B-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41B - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36B - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39A - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40B - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-40B-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39B - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36A - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40A - 2.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36A - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41A - 3.dat-pride.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-36A-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-38A-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-3.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-14-NSN-39A-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41B - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39A - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39A - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40B - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41B - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38B - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40B - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38B - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38A - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40A - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36A - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36A - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 40A - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39B - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36B - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 39B - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 36B - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 38A - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41A - 2.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15 - NSN - 41A - 3.dat-pride.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36A-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38A-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40B-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-38B-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39B-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-36B-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-3.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-40A-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41A-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-39A-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/05/PXD000743/2014-03-15-NSN-41B-2.datprimaryOK200003490jje@mb.au.dkNadia Sukusu NielsenMass SpectrometryShotgun proteomicsMatrix Science Mascot 2.3.02EyelidOrbitLaser capture microdissectionAmyloidosisConjunctivaMass spectrometryhttp://www.ebi.ac.uk/pride/archive/projects/PXD000743EyelidOrbitConjunctivaProcuring of amyloid deposits was performed as previously described. Shortly, 8 µm thick tissue sections of formaldehyde fixed and paraffin embedded tissue were cut and placed centrally on non-charged glass slides, followed by deparaffinization, staining with Congo red, and dehydration using standard histological procedures. The Arcturus Autopix Laser Capture Microscope (Applied Biosystem) was used to isolate amyloid deposits appearing red due to the Congo red staining. In addition, tissue with no apparent amyloid deposits was likewise procured and used as control tissue. Tissue was collected on CapSure Macro LCM Caps (Applied Biosystem), subsequently placed in sterile 0.5 ml Eppendorf Biopur Microcentrifuge Tubes (VWR) and stored at -80°C until further processed. Proteins from the laser capture microdissected eyelid, conjunctival and orbital tissue samples were extracted using a modified protocol of the Liquid Tissue MS Protein Prep Kit (Expression Pathology Inc., Gaithersburg, MD). LCM films containing captured plaque and control tissue samples were stripped from the caps and incubated with 40 µl extraction buffer (10 mM Tris, pH 7.8, 0.1 % RapiGest (Waters)) at 95 ˚C for 90 min. Samples were centrifuged at 10.000 × g for 1 min and subsequently cooled on ice. Extracted proteins were incubated with 5 µg porcine trypsin (Sigma) at 37 ˚C for 16 hours, vortexing every 20 min for the first hour. Samples were then centrifuged at 10.000 × g for 5 min, supernatant isolated and incubated with 10 mM DTT at 95 ˚C for 5 min followed by incubation with 30 mM iodoacetamide for 15 min in the dark. Peptides generated from each digest were acidified with 5 µl of 5% formic acid and recovered using Stage-tips (Proxeon, Thermo Scientific). The peptides were eluted with 10 µl 70 % acetonitrile, and subsequently lyophilized before dissolved in 12 µl 0.1 % formic acid. The samples were subsequently analyzed by LC-MS/MS using nanoflow liquid chromatography on an Easy-nLC system (Thermo Scientific) coupled directly to a TripleTOF 5600 mass spectrometer (AB Sciex). Samples were loaded on a 0.1x21 mm C18 trap column and a 0.075x150 mm C18 analytical column (NanoSeparations). Peptides were eluted and directly electrosprayed into the mass spectrometer using a 60 min gradient from 5-40% acetonitrile in 0.1% formic acid at a flow rate of 250 nl/min. Data was acquired using an ion spray voltage of 2.6 kV, curtain gas of 30, and an interface heater temperature of 150 °C. For IDA, survey scans were acquired in 250 ms, and as many as 50 product ion scans were collected if exceeding a threshold of 125 counts per second (counts/s) and with a +2 to +5 charge-state. A sweeping collision energy setting of 40 ± 15 eV was applied to all precursor ions for collision-induced dissociation. Dynamic exclusion was set for ½ of peak width (~6 s), and then the precursor was refreshed off of the exclusion list.PrideNot availableiodoacetamide derivatized residuemonohydroxylated residueThe mass spectrometry data was processed and Swiss-Prot database was queried using an in-house Mascot search engine (Matrix Science, London, England version 2.2.06) with a peptide tolerance of +/- 10 ppm, MS/MS tolerance of 0.2 Da, carbamidomethylation of cysteine residues as a fixed modification, methionine oxidation and proline hydroxylation as variable modifications, semiTrypsin as enzyme, 1 missed cleavage was allowed and ESI-QUAD-TOF mass spectrometer was selected as instrument. The Mascot search results were imported to the MS Data Miner (MDM) software with an ions score cut-off value of 45. MS/MS spectra validation of protein identifications based on less than 2 unique peptides with ion scores less than 100 were validated automatically in MDM and manually. Only MS/MS spectra containing a consecutive b or y-ion series of at least 3 fragments were accepted in MDM. The remaining MS/MS spectra of protein identifications were manually validated as only spectra containing a clear sequence tag of at least three consecutive residues with high intensity compared to the background were accepted. The data was then exported to excel and contaminating exogenous proteins were removed. Among these human tryptic peptides identical to porcine tryptic peptides were considered as contaminants as porcine trypsin was used for sample processing. The resulting endogenous proteins were listed according to their emPAI values, which reflect their relative abundance. The molar fractions of the endogenous proteins were calculated by dividing the emPAI value for each identified protein with the total emPAI value.ProteomicsJan J. EnghildTripleTOF 5600COMPLETEDepartment of Molecular Biology and Genetics, Aarhus University, DenmarkHomo Sapiens (human)26500418 Nielsen NS, Poulsen ET, Klintworth GK, Enghild JJ. Insight into the Protein Composition of Immunoglobulin Light Chain Deposits of Eyelid, Orbital and Conjunctival Amyloidosis. J Proteomics Bioinform. 2014 Suppl 8 10.4172/jpb.S8-002nsn@mb.au.dkBiomedicalAarhus University10.6019/PXD000743Amyloidosis is a disease characterized by the formation of extracellular amyloid deposits. Immunoglobulin light-chain amyloidosis can appear as a local disorder presenting with mild symptoms or as a life threatening systemic disease. The systemic form of immunoglobulin light-chain amyloidosis is the most common type of amyloidosis in western countries although it is a rare disease. Identification of the proteins forming amyloid fibrils is essential for the diagnosis of the disease and knowledge about the overall protein composition of the deposits may lead to a larger understanding of the deposition events thereby facilitating a more detailed picture of the molecular pathology. In this pilot study, we investigated the protein composition of amyloid deposits isolated from human specimens of the eyelid, conjunctiva, and orbit. Deposits and internal control tissue (patient tissue without apparent deposits) were procured by laser capture microdissection. Proteins in the captured amyloid and control samples were quantified by liquid chromatography tandem mass spectrometry using the label-free exponential modified Protein Abundance Index (emPAI) method. Immunoglobulin light chain kappa or lambda was found to be the most predominant protein in the amyloid deposits from the eyelid, conjunctiva, and orbit. Five proteins, apolipoprotein A-I, carboxypeptidase B2 (TAFI), complement component C9, fibulin-1 and plasminogen were found solely across all amyloid but not in the control tissue. In addition, the protein profiles identified apolipoprotein E and serum amyloid P component to be associated with the immunoglobulin light chain deposits across all three tissues analyzed. The method used in this study provided high sensitivity and specificity for the type of amyloid and may provide additional information on the pathology of the amyloid deposits in the ocular tissues studied.Insight into the Protein Composition of Immunoglobulin Light Chain Deposits of Eyelid, Orbital and Conjunctival Amyloidosis.Nielsen Nadia Sukusu NS, Poulsen Ebbe Toftgaard ET, Klintworth Gordon K GK, Enghild Jan J JJWater, mantle cell, sodium salt, Microdissection, Formol, ammonium formate, 13C-labeled, IL1BC, cadmium salt, MeCN, ion, CASP-1, magnesium formate, monosomy 2q32, Apaf-1, zinc salt, 5730420M11Rik, Polypeptides, palpebra, protein polypeptide chains, KL receptor activity, systemic amyloidosis, cobalt(II) formate dihydrate, Methanal, Parafilm, CH3-C#N, Microdissections, B1, SCO5, 3, SCO1, germacrene A synthase activity, Gsfsow3, Il1bc, CG10850, amyloidosis, SET, hac-1, phosphatase 2A inhibitor I2PP2A, Tissue, Oxomethane, proteins, W, IL-1BC, AI047805, DmelCG4299, PA1, set, h, column, infertility, D1, Red, RED, CT, Bs, monosomy 2q32-q33, stage, palpebrae, Histological Labeling, nickel salt, LC-MS2, Caspase-1 subunit p10, cobalt (+2) salt, Ct, anon-53Fa, Liquid Chromatography, l(2)SH0173, GAST, not genetically inherited, collisionally activated dissociation, CSA2, HMG-CoAR, CID, DmelCG7788, PBT, sodium (4:1:1) salt, Dm1, magnesium salt, SATB2-associated syndrome, Del(2)(q32), simple tissue, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, CG6829, dark/hac-1/dapaf-1, pbt, 2q32q33 microdeletion syndrome, Amyloid Substance, amyloidoses, HLA-DR-associated protein II, DI-2, I-2Dm, disodium salt, caps1, mantle zone lymphoma, formate, blephara, cromium (+3), inhibitor of granzyme A-activated DNase, study protocol, beta Trypsin, Apc5, APC5, I-2PP1, Speed, lymphoma, TAF-IBETA, liquid chromatography-tandem mass spectroscopy, Drice, ammonium (4:1) salt, TAF-Ibeta, methyl cyanide, DRICE, lead (+2) salt, PEP, krk1, Laser Capture, breadth, l(1)VE614, nickel formate dihydrate, lead formate, 1-Naphthalenesulfonic acid, DrIce, DrICE, developmental stage, aluminum salt, 2-trans, Amyloid Fibril, precursor, protein-containing complex, Chalk, body system, CG7826, SATB2 syndrome, LC-MSMS, Gene Products, CG7835, CG42273, amyloid, system, sterile, anatomical systems, thallium (+1) salt, PCE-2, beta-Trypsin, rubidium salt, 2pp2a, DmelCG10850, methanoic acid, ions, kf, CG10574, 2PP2A, Formalin, laser-assisted microdissection, Caspase-1 subunit p20, dSET, dSet, peptidos, MCL, 3'-((1, PTHB1, Reproductive, proto-oncogene c-Kit, dark/dapaf-1/hac-1, 4'-diylbis(azo))bis(4-amino)-, 1-(14)C-labeled, caspase 3, dApaf-1, Proteins, D10Wsu136e, Stainings, potassium formate, CE-2, copper (+2) salt, acetonitrile, buffer, (+)-(10R)-germacrene A synthase activity, polypeptide, formaldehyde, APAF1, native protein, Temperatures, Hac-1, I-2PP2A, KIT ligand receptor activity, C18, cupric formate, Dm I-2, Infertile (finding), Laser Capture Microdissections, infertility disorder, LCM, aluminum formate, amyloid disease, XKrk1, Fibril, AU020952, lithium formate, Ntup1, Dark/Dapaf-1/HAC1, IL-1 beta-converting enzyme, ethanenitrile, Interleukin-1 beta-converting enzyme, CD117, REDK, ME-IV, plan specification, 1'-biphenyl)-4, classical mantle cell lymphoma, Gene Proteins, Fibrils, Oxomethylene, C-Kit, Ssm, Sterility, Stress, blepharon, xkl-1, liquid chromatography tandem mass spectrometry, PE, AI450383, biopsy, liquid chromatography tandem mass spectroscopy, Hac-1/Dark, IPP2A2, Meth, NCMe, PreP, DmelCG6829, zinc formate, CG7788, crice, lead salt, protein, Xkl-1, AA410010, peptide, Cut, Gsfsco1, ammonium tetraformate, peptido, l(1)7Ba, l(1)7Bb, Congo, Pop, Min, Apaf1, cytopathology, protein aggregate, monosomy 2q32q33, Gsfsco5, ARK, DmelCG42273, SOW3, Eyelid, portion of tissue, LCMSMS, precursor ion., reference sample, peptides, TAF-I, Formaldehyd, min, arc, mAPC, Substance, mantle cell lymphoma, copper, Amyloid, ark, CG11387, T1, IGAAD, chromosome 2q32-q33 deletion syndrome, lithium salt, DmelCG10574, Ice, ICE, Pathologies, C16orf53, dApaf1, Sl, ammonium (2:1) salt, Capture Microdissection, (+)-germacrene A synthase activity, phapii, sterility, Ida, IDA, Water Stress, ice, iCE, D-Apaf-1, drice, LC-MS/MS, mKIAA1121, Dmel_CG7826, StF-IT-1, Tr-kit, Labeling and Staining, infertile, Thermo Scientific, Cryopyrinopathy, Amyloid Fibrils, glass, MP-1, Ionen, drIce, drICE, tissue portion, kl1-A, BcDNA:GH10590, KIT, GAS, nickel (+2) salt, fixed, Dmel_CG7835, CAPS1, Crystal, Mnb, MNB, parent ion, tyrosine-protein kinase Kit, ammonium salt, histopathology, caps, P45, cobaltous formate, Del(2)(q32q33), AI047692, mKIAA1104, kit, hac1, CG4299, gas, AW124434, organ system, dapaf-1S, LMD, apaf-1, dapaf-1L, Labelings, precursor ion, Acetamide, copper salt, MP1, p45, Polypeptide, l(3)SH7, Laser, eye lid, fertility disorders, i2pp2a, CAPS, Capture Microdissections, Dapaf-1/HAC-1, Infertile, Histological Labelings, cesium salt, SCF receptor activity, Gene, PHAPII, LC-MS-MS, CADPS1, Buffer, formic acid, Dark/Hac-1/dApaf1, method, Hac1, potassium salt, Dark/Hac-1/dApaf-1, polypeptide chain, scfr, template-activating factor I, glass syndrome, 14C-labeled, method used in an experiment, Tina, Histological, SCFR, hYAK3-2, Fdc, Glass, Staining, iones, Formaldehyde, amyloidosis (disease), ipp2a2, dapaf-1, dapaf, dark, calcium formate, DmelCG11387, DARK, taf-ibeta, Reproductive Sterility, liquid, cromium (+3) salt, dArk, Dapaf-1, 2-iodo-, sodium formate, Controlled, DYRK5, 2q32-q33 microdeletion syndrome, Controlling, DYRK1, data, nickel formate, 2q32q33 microdeletion syndromes, AU067781, 3H-labeled, protein complex, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, igaad, strontium formate, apaf1, strontium salt, Labeling, Peptide, light amplification by the stimulated emission of radiation, LC/MS/MS, CAD, Sterile, natural protein, Protein, I2PP2A, l(3)63Fb, FORMALIN, Dyrk1, CES2A1, Dark, connected anatomical system, Dark/Apaf-I, ACETONITRILE, FORMALDEHYDE, cyanomethane, SAS, c-KIT, CC1, Tripcellim, 2310012C15Rik, dApaf-1/DARK/HAC-1, Methylene oxide, chromic formate, incised, Protein Gene Products, Interleukin-1 beta convertase, Trypure, dSET/TAF-Ibeta, c-kit, 2610030F17Rik, Ion, 3.4.22.36, calcium salt, Peptid, AA407739, dAPAF-1opsonin activity, Visible Radiations, Radiations, Eyelid, amyloidosis, Visible Radiation, Radiation, amyloidoses, HVEML, HVEM-L, Lichtquant, amyloidosis (disease), Photoradiation, blephara, Visible Light, Light, Visible, CD258, LTg, Ly113, antibody, immunoglobulin, palpebra, ch, systemic amyloidosis, light quantum, Amyloidoses., LIGHT, Photoradiations, hnu, blepharon, B cell receptor activity, photon, amyloid, TR2, light, eye lid, foton, palpebrae, amyloid disease, gamma1100001C23Rik, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, l(1)VE614, human being, 2310074I15Rik, ion, AW549739, D330041I19Rik, instrument configuration, FEZL, L Isomer, cleavage, Gene, protein, Spectrum Analyses, Computer, protein-containing complex, high intensity, peptide, Polypeptides, Cut, L-Isomer Methionine, protein polypeptide chains, hydroxylation, Drug Tolerance, Methionine, ClvPrd, peptido, polypeptide chain, TOF, l(1)7Ba, l(1)7Bb, L-Proline, Mass, Gene Products, L-Methionine, Software Engineering, Analysis, Half-Cystine, protein aggregate, keratosis palmoplantaris transgradiens of Siemens, transgrediens palmoplantar keratoderma of Siemens, Pedameth, Computer Program, Mass Spectroscopy, ZNF312, Meleda disease, Application, ASD2, C79691, Mass Spectrum Analysis, ARS, Open Source Softwares, Search Engines, peptides, Analyses, TACHD, L Cysteine, M, Software Application, iones, AF006999, Open, beta-Trypsin, Open Source Software, Computer Programs and Programming, Sciences, proteins, ESI, ions, kf, man, CG11387, ArsB, Computer Software Application, Lccp, MAL DE Meleda, mKIAA0989, mal de Meleda, 2-amino-4-(methylthio)butanoic acid, 10^[-6], Tools, DmelCG11387, ppm, L Proline, shru, sample, CT, peptidos, Half Cystine, metionina, Racemethionine, FEZ, drug tolerance, Applications Software, Open Source, data, Computer Software, Zinc Cysteinate, DL-Methionine, Molars, protein complex, immune system tolerance, molar, Proteins, 2-Amino-4-(methylthio)butyric acid, Ct, ANUP, Search, MDM, L-Isomer, Spectrum Analysis, Peptide, results, Source Softwares, Engine, 2310057K23Rik, Software Tools, Tool, Programs, Spectroscopy, polypeptide, Program, Computer Applications, Software Tool, Immune Tolerance, native protein, Ionen, natural protein, dens molaris, Computer Applications Software, Protein, Computer Applications Softwares, Immunologic Tolerance, sequence, Methionin, methionine, Hmet, Softwares, background, mdm, BcDNA:GH10590, Hydroxylations, Software, Mass Spectrum Analyses, Data Base, Met, Mass Spectrum, VSD1, 2310036G12Rik, Software Applications, LY6LS, instrument, Protein., Source Software, Engineering, Spectrometry, AV006427, Tripcellim, D830007G01Rik, MASCOT, L-Cysteine, beta Trypsin, primary structure of sequence macromolecule, human, sample population, introduction, incised, Protein Gene Products, Computer Programs, Gene Proteins, Trypure, ZFP312, Applications, Self Tolerance, Applications Softwares, Tolerance, clear, hyaline, Ion, L56, keratosis palmoplantaris transgrediens of Siemens, alpha-amino-gamma-methylmercaptobutyric acid, Peptid, Polypeptide, variable, Liquimeth, Immunological Tolerance, Computer Software Applicationsliquid chromatography tandem mass spectroscopy, Forms, Microdissection, Antemortem Diagnosis, Visible Light, protein, Amyloid P-Component, Serum, Diagnosis, Readability, palpebra, protein polypeptide chains, systemic amyloidosis, diseases, Microdissections, hnu, symptoms, diseases and disorders, cytopathology, Analysis, protein aggregate, foton, Primary Systemic, multicellular organismal biosynthetic process, Mass Spectrum Analysis, Eyelid, Immunoglobulin Light chain Amyloidosis, portion of tissue, amyloidosis, single-organism biosynthetic process, human disease, LCMSMS, reference sample, Analyses, anabolism, entire life cycle, Serum Amyloid, Tissue, proteins, Substance, Amyloid, free, ch, Pathologies, Homo sapiens disease, associated, palpebrae, Diagnose, Capture Microdissection, Amyloidoses, gamma, LC-MS2, screening, apolipoprotein, Radiation, LC-MS/MS, Immunoglobulin Light-chain Amyloidoses, Light, Spectrum Analysis, Diagnoses, Spectroscopy, Amyloid Fibrils, Postmortem, LIGHT, Apolipoprotein, Examinations and Diagnoses, Diseases, tissue portion, simple tissue, Primary Amyloidoses, Postmortem Diagnosis, Visible Radiations, Diagnoses and Examination, Postmortem Diagnoses, Epistemology, Visible Radiation, Amyloid Substance, amyloidoses, histopathology, HVEML, life, Systemic Disorder, Spectrometry, signs, common, blephara, human, LMD, disease, immunoglobulin, light quantum, Specificity and Sensitivity, AL Amyloidosis, liquid chromatography-tandem mass spectroscopy, Systemic Disease, Primary Systemic Amyloidosis, eye lid, Laser, Amyloidosis, other disease, Laser Capture, lifespan, human being, Capture Microdissections, lipophorin, Systemic Amyloidosis, Gene, biosynthesis, Amyloid Fibril, Spectrum Analyses, protein-containing complex, LC-MS-MS, Serum Amyloid P Component, Ly113, Amyloid P Component, antibody, method, polypeptide chain, method used in an experiment, LC-MSMS, Gene Products, Mass, disease or disorder, Primary Amyloidosis, amyloid, light, Antemortem, Mass Spectroscopy, study, formation, entire lifespan, Lichtquant, amyloidosis (disease), Diagnoses and Examinations, Visible, man, non-neoplastic, synthesis, AL Amyloidoses, laser-assisted microdissection, photon, disorder, Sensitivity, Primary Systemic Amyloidoses, TR2, Controlled, Antemortem Diagnoses, Controlling, findings, protein complex, Systemic Amyloidoses, Proteins, disorders, medical condition, Primary, CD258, Examination and Diagnoses, Immunoglobulin Light chain, LC/MS/MS, Amyloidoses., native protein, natural protein, P Component, Protein, Laser Capture Microdissections, condition, LCM, amyloid disease, Mass Spectrum Analyses, Fibril, opsonin activity, Radiations, Immunoglobulin Light-chain, P-Component, Mass Spectrum, HVEM-L, Photoradiation, Specificity, patient, Understanding, LTg, Protein Gene Products, plan specification, extracellular, Gene Proteins, Fibrils, Photoradiations, systemic disease, Indexes, blepharon, B cell receptor activity, liquid chromatography tandem mass spectrometry, biopsyPilot, liquid chromatography tandem mass spectroscopy, Forms, Microdissection, orbit/MAST, thin aggregative fimbrae, Antemortem Diagnosis, Apolipoprotein AI, conjunctivas, 0686/07, Arginine Carboxypeptidase, Carboxypeptidase B2 wt Allele, C elegans, Eye, A4, Visible Light, protein, conjunctivae, Amyloid P-Component, Serum, Diagnosis, orbit, Apolipoprotein A1, Apo A-I, Readability, palpebra, protein polypeptide chains, systemic amyloidosis, diseases, Apolipoprotein A 1, Eye Socket, Microdissections, hnu, symptoms, Bulbar Conjunctiva, Project, diseases and disorders, orbit/mast, cytopathology, protein aggregate, eye socket, Apo A-1, foton, Primary Systemic, multicellular organismal biosynthetic process, Eyelid, Immunoglobulin Light chain Amyloidosis, portion of tissue, Apolipoprotein A I, amyloidosis, single-organism biosynthetic process, Fbln1 protein, human disease, LCMSMS, reference sample, anabolism, entire life cycle, orbit of skull, Proapolipoprotein AI, CPB2 wt Allele, tunica conjunctiva, Serum Amyloid, Tissue, proteins, Substance, Bulbar, Amyloid, fbl-1 protein, free, Pilot Project, 1-Plasminogen, ch, Glutamyl, Thrombin-Activable Fibrinolysis Inhibitor, Pathologies, Pro-Apo A-I, Homo sapiens disease, associated, Thrombin Activatable Fibrinolysis Inhibitor, palpebrae, Chb, Diagnose, Capture Microdissection, Amyloidoses, Socket, gamma, LC-MS2, screening, mast/orbit, apolipoprotein, CLASP, Radiation, NEST:bs17d05, Tissue., LC-MS/MS, mouse, Immunoglobulin Light-chain Amyloidoses, Thrombin-Activatable Fibrinolysis Inhibitor (TAFI), Apolipoprotein A-I Isoproteins, Light, Carboxypeptidase B2, anon-WO0104295, Diagnoses, Amyloid Fibrils, Orbit, Postmortem, LIGHT, Apolipoprotein, Examinations and Diagnoses, Diseases, tissue portion, simple tissue, Primary Amyloidoses, Pro Apolipoprotein A I, Postmortem Diagnosis, CG32435, Visible Radiations, Diagnoses and Examination, Postmortem Diagnoses, Epistemology, Visible Radiation, Amyloid Substance, mast, amyloidoses, histopathology, HVEML, Apolipoprotein A-I Isoprotein-4, Projects, Plasma Gene, Orbits, Pro Apo A I, Plasma Procarboxypeptidase B, life, Systemic Disorder, clasp, signs, common, blephara, MAST, Palpebral Conjunctiva, human, orb, LMD, disease, Rare, immunoglobulin, DMDA, light quantum, Specificity and Sensitivity, AL Amyloidosis, liquid chromatography-tandem mass spectroscopy, ApoA-1, Systemic Disease, Pilot Study, Sockets, ApoA-I, Apolipoprotein A-I Isoprotein-2, Primary Systemic Amyloidosis, eye lid, Laser, Amyloidosis, Orphan Diseases, Plica Semilunaris of Conjunctiva, Plicae Semilunares of Conjunctiva, Apo AI, PCPB, other disease, Laser Capture, Eye Sockets, Apolipoprotein A I Isoprotein 4, lifespan, human being, Capture Microdissections, lipophorin, Glu-Plasminogen, Systemic Amyloidosis, Gene, apo-AI, biosynthesis, Amyloid Fibril, protein-containing complex, Glutamic Acid 1 Plasminogen, TYPE, EC 3.4.17.20, LC-MS-MS, Serum Amyloid P Component, Ly113, Amyloid P Component, DAGA4, antibody, method, polypeptide chain, method used in an experiment, LC-MSMS, Gene Products, Studies, disease or disorder, Primary Amyloidosis, Mast, amyloid, Glu Plasminogen, light, Plasma Carboxypeptidase B, pCPB, Antemortem, MAM, SCG3, Plasminogen, Pro-Apolipoprotein A-I, BcDNA:LD31673, Orphan Disease, CPB2, study, TAFI Measurement, formation, bony orbit, entire lifespan, apolipoprotein A1, Lichtquant, CPB2 Measurement, amyloidosis (disease), MAST/Orbit, Diagnoses and Examinations, Visible, Procarboxypeptidase U, man, non-neoplastic, synthesis, Study, Carboxypeptidase R, AL Amyloidoses, Tunica Conjunctiva, fibulin 1 protein, laser-assisted microdissection, Conjunctiva, BM-90 protein, photon, disorder, Sensitivity, Primary Systemic Amyloidoses, v40, TR2, DMAP160, Apo A1, Carboxypeptidase U, wall of conjunctival sac, MESR7, Controlled, Apo A I Isoproteins, Plasma Carboxypeptidase B2, Antemortem Diagnoses, Disease, Controlling, findings, CPU, protein complex, Systemic Amyloidoses, Proteins, disorders, Apo A-I Isoproteins, medical condition, Primary, Palpebral, Carboxypeptidase B2 (Plasma, NEST:bs28g05, CD258, Examination and Diagnoses, LGMD2C, Glutamyl Plasminogen, Immunoglobulin Light chain, Carboxypeptidase R Gene, LC/MS/MS, native protein, natural protein, APOA1, P Component, Orbit/Mast, Protein, Thrombin-Activatable Fibrinolysis Inhibitor, FBLN1 protein, DmelCG32435, Glutamic Acid, Laser Capture Microdissections, condition, LCM, amyloid disease, Fibril, Rare Disease, opsonin activity, Radiations, Immunoglobulin Light-chain, Plasma, P-Component, Glutamic Acid 1-Plasminogen, NEST:bs13a06, tafi, DMDA1, CPU Measurement, Carboxypeptidase B-Like Protein Gene, Orbit/MAST, HVEM-L, Apolipoprotein AI Propeptide, Apolipoprotein A I Isoproteins, Profibrinolysin, Photoradiation, Specificity, Conjunctivas, patient, TAFI, Understanding, LTg, Apolipoprotein A-1, Protein Gene Products, plan specification, Orphan, extracellular, Gene Proteins, chb(v40), Carboxypeptidase B2 (Plasma) Gene, Fibrils, Photoradiations, systemic disease, Indexes, SCARMD2, blepharon, B cell receptor activity, liquid chromatography tandem mass spectrometry, biopsy, Apolipoprotein A I Isoprotein 2, Carboxypeptidase U) Gene, Pilot Studies, Carboxypeptidase B2 Measurementopsonin activity, Visible Radiations, Radiations, Eyelid, amyloidosis, Visible Radiation, Radiation, amyloidoses, HVEML, HVEM-L, Lichtquant, amyloidosis (disease), Photoradiation, blephara, Visible Light, Light, Visible, CD258, LTg, Ly113, antibody, immunoglobulin, palpebra, ch, systemic amyloidosis, light quantum, Amyloidoses., LIGHT, Photoradiations, hnu, blepharon, B cell receptor activity, photon, amyloid, TR2, light, eye lid, foton, palpebrae, amyloid disease, gamma349trueInsight into the protein composition of immunoglobulin light chain deposits of eyelid, orbital, and conjunctival amyloidosis.Amyloidosis is a disorder characterized by the formation of extracellular amyloid deposits. Immunoglobulin light-chain amyloidosis the most common form of amyloidosis can appear as a local disorder presented with mild symptoms or as a life threatening systemic disease. Identification of the proteins forming amyloid fibrils is essential for the diagnosis of the disease and knowledge about the overall protein composition of the deposits may lead to a larger understanding of the deposition events thereby facilitating a more detailed picture of the molecular pathology. In this study, we investigated the protein composition of AL amyloid deposits isolated from human eyelid, conjunctival and orbital specimens. Deposits and internal control tissue (patient tissue without apparent deposits) were procured by laser capture microdissection. Proteins in the captured amyloid and control samples were identified by liquid chromatography tandem mass spectrometry and subsequently quantified using the label-free mass spectrometry quantification method exponential modified Protein Abundance Index. Immunoglobulin light chain kappa or lambda was revealed to be the most predominant protein in the amyloid deposits. In addition, the protein profiles identified apolipoprotein E and serum amyloid P component to be associated with the immunoglobulin light chain deposits across all three tissues analyzed. The method used in this study provides high sensitivity and specificity of typing amyloidosis and may provide additional information on the pathology of amyloidosis.2014-05-292014-03-20PXD0007432806551646099180498511145422492156843544071284218327042363336351198343006636362758385696363121766668888111430155571145263145262364934613126957366649239161936413645106656889511363647627236611123294422295558326813042323122586365434607925193659106321432059712938655819125023254537111957748186619682158672256807617554373592536685862740816918045427877512010892250583674147956410039236942049433445974142001258641935293NCBITaxon:776436715675936438677160540483131528269304562716391624292042779447623763696121810032962922113763948840479NCBITaxon:2157131527310510671250278205968720165163684071736309698936104782148364320429294101061320491381693743277320464535111103217459216129288671288676410069456941016763410210761277351131658213584301417298174633675412873567568403013506218130194111929439367110411364459139498432025301270320221498751104759412047886134749515372110971652998279051355513980317585439801260866398081375755518320196447111415542193255521138343911931819813981810269701069955529NCBITaxon:47518502983354764146547798251021691572739823897648407413735186287054824153NCBITaxon:50557984467525100036433414754802103597413708115466547898353221599838106771034819852348780422531488414222863226634794615718712593991599191572952929211752719860148840633424951869123423523815233598589859886559746499870392021110723635272159874190828743418235024145113969293190259390719017463601237474636172262536001319722119158531058859698951105198997237989772000263419610264266722758858156899628737562690724420237172019998570724074767927459615333554319311671833554184005136861505968666211961748666134751536329NCBITaxon:176328628711033348837670580271848186536859598607575527472036105135294296110098402321000734882412336363071047005187878945556449447NCBITaxon:13356262664955419591399878168119011478281055524NCBITaxon:960613585846900813668481979153519307285930085264114090051184995262254121337591390143811139442370416744312044143708351581990119519532590841370137023943222774862615835583715371633376057267998086371137121906503714759172073127262981274575727090309031637910372814243371421044792491108239412NCBITaxon:961565885814780269266100658137352750454135663816475203750644223669502129349790546322455525365199764990814389923745374726473237602647312887055955361416915252740327160293851149786479436375529382479437225117752991204474167387217509193844137659393432715910022637674234442345467001287689591198467041464792936528034280382803510803481793921126212295027113118037386819112652699710286225273910760159736114324250711409810871355477436581424507229533796982042321242233218033698223470816457331858897165467599287770203829314125295508114817448886437452649997283035718308550717629970767892683704151562887651388563924561152086595551655181135491432137159749535026143213858781707683194963401614280053164686275110466038151845474485009747697477118051240174841855601555479204274201488711053253297261005941289093164351211604990013894382835423242331082934122058560416299131122731701879915429131267818187104931640729946714423683033373304852646383011306413992530642369923121162065261610337286129940207340115357652611114716133865431201725323712552329935316317NCBITaxon:1108499384106326787286232193348620862116079139222768119612552281495393213223233477412182753291757312994886181408434103351996313924891392488115338115339330439375569928626559933911209488624157183997586444237486435332444260665332413439097682127178637197985686399983998686553529148654104298635735825763288401986498238011191102868899958665220341632138119380625631886571303443112130886581144889198466645463NCBITaxon:11072NCBITaxon:11071142800628835374375116597145943116598854331116781077854314408043933434NCBITaxon:11082693977381382189931824431935128387145953116885311213278695berry8694100333586972443664701501114286921504751499105484204714722354025120847014649744497431170089306218644193061107632330805660396016217974825853946055396513212790568813377512981766017112147861050236694657349632051124501897441739412450128853183889198679488531911137910371647351660152943631631198573896939343237956026087121346334323223544314275241433611334565560291699636436802790105603140818838185733703401881274414437552196969716203871398558408172405598609183827275921274423408170275981274420127442623545513656533821176275943282474801199150956481882291690255120455148167238473848190695148498101510693731263753405203860186497405224052141856451804NCBITaxon:81347800915227548479387033384938719172261756109461614351203258120550523525944732054938641125722651216512538803766861206781122022307432201186705118670573873348691219387918680239800718680121545146835140818615084712067776918388516086113888691521677867212790100870435123171969281239294867713315484542261262198131882682411229265716329576938124712461485451328388348392949113903631204162665890771514880036942694169436945187901015080817053942065421055687317447127015329242814111946691169601454586953201019812646905505371408157697392830312383911283128212802811010832825253531522811235315349825741948153623142410145481NCBInr 2013051929459706473129212885757739803130980089149697810369012202075660173654856615664103695118702118705226186129952694565621721956581010286560615659656064432942838656717136041602358700150480210029132529111870014477166418091325292699756653663056661348879379651431340223926633636336613833663367111764531434510378905923213143448709767468NCBITaxon:405597674651419842359093226411320498217870749821634725656905691569256934362872249821187205697111327949928993002014538661410NCBITaxon:493230540087155689871710005898732135248304611308126373039114398872532897187268723872487298727135293324223110677410677330554831791988224454461041059098824974736776787524875217082485578418724632819632224194439105402104547815805968628606100264462NCBITaxon:548681546414394503307734875152600875987563232593354813057372024849100107726756726756643061543194721726514492394704721122984476119152361088767NCBITaxon:12978848313987828658597454129314289864801262834854189854875630411301361182599495291201327986491146247274601735272855525263852639119813330240976392465732252641109094674694163485131535231523845NCBITaxon:5659951736582200879325731399034651329196114644042479096109760616125732927294227294327294451338510516943146128017646571186961186941436183118698266264118691443906NCBITaxon:777156633840433061851908025687034851025731025731156870861822305479186786618351350NCBITaxon:780390645151599031645151610406109431292573091930791094460913749440061982587412747078202040661923915NCBITaxon:714130951334347044830064192389003715908412810840697228233428104392011323902320821097797481140686251093928670620049291026339321034809109314140674109784257546013076376619108049267NCBITaxon:9874276892275081214822126719411462104905619922595767748371NCBITaxon:7227156974370031263406591090130327697411476130941147013081307383234114793981105268513141313131139655397210184141148345504539911009845262724153009107662041149013037134441439832747003988136416435623136417216895137743928668390614404211945993365399490336578618533658431275316273316277135280869135199488316275502779994871679718207954134966002713062744894831549675502780443239660025304292366522570212721349163349161135913581716741928434239549414717414718156269857301182590247149456092828513356262836999286757226404595374575740574113467611233523785481168511335638126216131091515429395920139613921390271489612881016010675744580240251229683352944139366581120866057625763443220667214082721200911408274282317729818431834432265755575757592810817066713640018399364442184922311210542111096976529818826331488373184319229438143124110497774438667825317513278042676085111022358801198732518519687916621411408224430491408223264561101411867631854312525985207677376777696871544580NCBITaxon:55710447226493298830NCBITaxon:177310117134634923166336745101161068873132842626587254231882915819546548883919436612336814498550554382641310338845106654119632756253232316856913494098855326424621017366041137138208452118565031575018516515210095715735457157511162348086377216315749620488678629627552319758258458533668510523110091100903487761009264653234063340621200793596106453913125757469242030690259374580465804227779189957319552491313662392410731300146625315684569374515479221198561198571462594NCBITaxon:592012676716248NCBITaxon:104385626994127915422231314781340388722921008810654976717589554930562791292491155748246787634291202531637616131477115200228569418679303971726507256117762876692026289931563430189714192234463433872227634364240206282366742138638842049321135472447314473111003169681112902551613983367225279310036NCBITaxon:11266NCBITaxon:439488186794414549413749901004163459106592106590NCBITaxon:6624427112390144270100498017410289415978688333295494252826521581094343265215780101279085256223727021654360507601435590763200359391305498008179536179535179534132234317953093551323674802293581890364395019825289839642711305311925231177189587753460523NCBITaxon:289011218948932172697049803113180803014179813052114505338918789184NCBITaxon:97047494080498040578822593191402434271283734256136141799714081406290028131567375433131641631591009714629774671446750601391726145051115249627487496846051926020158002153818625622692756142314224279242751119276714505201017552759142826641799069141746091117977712920369408252824582762167539131463977852714273507145134073203696223283580712296213754513678303976630867837109458015802295358146213335241798193109461942024527882787809036809933084581058111524260NCBITaxon:128056189618726351472640319520657467073884133853881354615821582390341390539034041377338152118099583310367265851149315242591130832263737NCBITaxon:127211488148558431043002451358472668342953195738261639945305861123817026683514981496452145225855452811320837514622191520896020896437950420896313797913871272838440066720327545326026447108803658674784342165992165972165954550323098216596216591169683314145321832175462713542424543587461517203094980194547752555697815950943984525338551534398990371228577595156226231121088624455513108058884558707791817808431796758144571160488409859NCBITaxon:371626794015059076303555463263331199456545671025426420126420352486769674939254727933428146488668760910874824577444917604893219172652579250167342810239559863258278839659444771604903552527313366366666810242669102431024575741786260349666452680126757776414579663136701908323311561808958355106766571927634123598744456220668350701134734264002113615718006655648433767760207214413792997671400820140082111557110897244447899665349148624614749312659219292951946751299114127647363267656589363589366192011577271208370265554809664098614098609958676686337137221171101107687834974120280913485851348584502539249910861913249943311711395037117082711708281144522197822446147940210195375939723287581721874202566481219071NCBITaxon:57390507911654564526591774208321387NCBITaxon:615750521028307155864505912466635761311887631088878176179212190659407121906712111044975151950585066NCBITaxon:25068NCBITaxon:120651187036126344695060506150627249124643248784461229417487812594798101819430108673101851018457303963558633149246437151458280321430801321650855534825534812607101856871416333NCBITaxon:619125164341121877812764515981284742163577553470951451225786425011260704278352607052607075730616584573677340541636774831672331505610071337056NCBITaxon:305550445719287512987222005482282912680631532734171929111167815022830NCBITaxon:2089642836617429483NCBITaxon:569382688306401794699138995915104352581515140129448242825844160419759272604232816772850120310267386492405360883858115589227054156224882936534036771861561088818817511935015075221193502167879108579172407132912122663060828805712561329013335503857917851310078752824NCBITaxon:610172433594633185862607991612432141262200298492670NCBITaxon:12637192812492125283038568385695911309632237561105025826662551519788360094338187146042235247269055614012575151111672085151546170296719445446415243235965489592022158010019995550884606157915781928650338921162089453593650917389440NCBITaxon:68544127541590109013410304158955210129661030612967142368715851584515849157592141038419286481928649369113388914792359046133296610914947616436902116022164133159936909108917688149229990894621812144640287889332952828294456861749342273218903824563201247190400727NCBITaxon:9913997828206411129167145372097152153588816715754626694026561940137105314120603281143193332912924792001292272573908726727103790857372921405329412816078393142626548982273779253905962073288273514312979360533079721980941159556406072414473352360971509493349334793604674776290318625673567026566977193357158053607699468810376103774162763870520037584349224282687303131425685007123038364940813430749414422197857742171598921409239396211577811547569297932447047499061035919051581144527499073129877754699110358NCBITaxon:372961036098334113079819643201336794133679578310340157865826453650591169654788546981343176432445861119529745531131316634305521329836031276129938505785056642615099019794011513458445771513461694009983512056234451455116761080772134879956962877827544667787218496209948873221849320972096209524831921188481441467761266447NCBITaxon:2697049509169369411031219588320509202906101580181306859458822499525297246741158933852894271188418942614774051108849356082567371233435514149317405534514451455147124546655334188925124679151641373345087711100832391290391295297196223127486931797891133731054876363271251985076255470222523118781386541204551655862238NCBITaxon:446649411324446493139458624212418730364926491141516784588108743952703195346232222690051671399669527106788954120030895442066563954530055862335518042643020030228481242642827283110299102981303873414452386262903195418329025862319557575584131016538235255772238235939946360106383689360104399483994786790094895154440423761082363557211622967718705473693128136011582451855794318682406672824932358255233271170621517271501261557228331314685349390NCBITaxon:1011428450297805952312735411437330959882674275295952664373427582243089593826094327495921122233295160520165108712169795252838697285290420425304274212187073347471323429278161685040119219297605821812498854695846312204397331639107243738545888587252049369295546480383436912243261241935595521749399128161204254655194582281933298297259557114317927284355285716481867346120724139961660187625436044829647187614378681490494514725457254272543176101214801541071031879936188294550303416123081663360361659840505693528354528353528352527021529456698742972257247725859410976771679812310061911079450950412694322710279434472568291146946362136521871448542334937347373495270004466449917591891582580433302448046260499NCBITaxon:129391080612461962902224619732063752299169450906811879475723077412581175780329031114727392952790931103683997844597240287475129513912624693399527132521034304319629172644813817818936081080228156100547625575995535011123491922221979111196866197912104072813951080230230603104014595416193419352821103264416105116071111702272104117063435127443210859562102831283166837283165597299495141065888271141131610584133087947844751742933877099643263033962841793277932941729341066184714575513925192323923206401311606201356661606212133242605339528518538470047873395910739961356742951056500242619115062182996339415486813469597538631211705193516265390021341885322497392162425159344334833482468822638632121969025016468606885126234777016669121513300305899105884500634349421608823578652224215745246729161321751267934065604642933114342808300181349865236526212633761186175831678733450736544345076166690510894491089448NCBITaxon:27596535520710894441045010447093655066897447094287535NCBITaxon:5833300692906526659581211776266595311786654913497675192964417725784544417711581419NCBITaxon:12066381666117467329073651668446896573346377960169944446859600NCBITaxon:58111182263477154119165784584840215530756636164034624136813497888518010893112686341428099612NCBITaxon:5820NCBITaxon:582126531155319921150857975522836801986373791966272905896059606446709603227086266596496042929195705091210454357253309050429170455429829387834810612793654483851074454191701134899615266599369169275736407821963257075298351036171206189257771285023308352701427869991417158779627300251102856312673615286964696439644441768NCBITaxon:114277746128113450696381715229965696577575017757871123869351746966222790963787576784218192119562330595216742697961344346360134519678668219676673840967712495153304394032246200330459669968583554767896839689342054557600968110428039320111678078330381719117630247593217181717475933NCBITaxon:102981257118387279694836470384766438467635688NCBITaxon:150270298207621158612184512107496866111495720928520131913840405295071263854614666383379NCBITaxon:10239173610629943630870547515851744575412NCBITaxon:1024528586NCBITaxon:1024317481565633788067067135622583313618550992452779658334240906112563049495NCBITaxon:631217707070100940869292570748761381765148942329032176023993521467529474629474743760317814465602853217738464517721774372725572725591534811215323690147266470913170472585209227976202697859628596312638712146972120353326483731532146935837069030749376083334833335704728511111497083332833315041221468710801874920063737350510428782801485175050426NCBITaxon:1155213992751562259311726231656777351116032932853422NCBITaxon:5759345089998103517307796407148457425457428121536024271875058NCBITaxon:104075678024271535242915954126291589203985781355886755122965879309458041920312410515358153985801331678906902725602725612214272563354422841027256434166379017904NCBITaxon:57963562NCBITaxon:694002NCBITaxon:69400935552222104577575596995926367140370216466101364CP010395.12242185732322392307419641640278489644720206937717566144036666102254400540296543NCBITaxon:117098046222469764992297936941638284593556182284590143673340353143673452763922611117957527640985986661362652816230610442179622490541565050176946996NCBITaxon:1313171250795338942795579594219722872285421925306612945704176724041889122088932088952075596645231521753153687983020041828860656725331139269635889NCBITaxon:13156730195388399227166665553256657123051120755534131359022491179986669400666684215767114353531151042983154689111298593273075660469136165105612149161522178523897633612149159704126308213288818831313613NCBITaxon:1865381889081916073NCBITaxon:1865366873039376527306855743615295266891057675358231223NCBITaxon:1383059594045840018591293585742917616089942917030027340542364126243232701547605681786064778161982159739998049755998024199474275774155933623713036814073407666701338881204104411117071111708299204072656367139612211450134408440877111745479778745461074019679496795701864081408238039452813516596686123517861624323124323013599235612710820347699785409640979788210352243277451574090978040924093447135298386157331781008163136253886541554018134168704364869796732399793299187137299119548629916713033456433169173623125924851221282861109464722641988479451332103721284813173144077217913169315557781221119778219512012215225025518365231818600781131323848571584645671591692259133349912496153345422432751204739243274536552134014364957165380207167849641673124966871601977162NCBITaxon:10357NCBITaxon:103581194881415784NCBITaxon:1035910458561707215976527263418593478341881882160321311344589499326276261969471634955913645272621272623272624116071912389931214102132474403217142118213144032449032483431114778749093238481437113153681286640136841491859799491154373440302780832823525174299218951929524929492249241262673967315187661533489673012328013603190304143401191102225174949324934110205319795391902112111439190451866361713907710619813530085592921486917198252157728141444818759449593625NCBITaxon:1167622413516343429110454952679895362726500418