Dataset Information

U1 Small Nuclear Ribonucleoprotein Complex and RNA Splicing Alterations in Alzheimer Disease

ABSTRACT: Comprehensive study of the human brain-insoluble proteome in AD by mass spectrometry. Mass spectrometry analysis of detergent insoluble fractions was processed based on our optimized LC-MS/MS protocol. Protein concentration was determined by bicinchoninic acid (BCA) assay (Thermo Scientific) using bovine serum albumin as standard, and further verified by Coomassie staining on a short SDS gel. Approximately 50 ug of protein per sample were resolved on a 9% SDS gel and stained with Coomassie blue. Each gel lane was excised into 20 bands followed by in-gel trypsin digestion. The resulting peptides were analyzed by LC-MS/MS (2 h) on an LTQ-Orbitrap mass spectrometer (Thermo). MS/MS spectra were searched against a human reference database from the National Center for Biotechnology Information using the SEQUEST algorithm (version 28). Identifications in Sequest .out files were converted into pepXML format using out2xml program of the Trans-Proteomic Pipeline (Institute of Systems Biology,Seattle, WA). Searching parameters included mass tolerance of precursor ions (+- 20 ppm) and product ion (+- 0.5 Da), partial tryptic restriction, fixed mass shift for modification of carboxyamidomethylated Cys (+ 57.0215 Da), dynamic mass shifts for oxidized Met (+ 15.9949 Da), three maximal modification sites and three maximal missed cleavages. Only b and y ions were considered during the database match. To evaluate false discovery rate during the spectrum-peptide matching, all original protein sequences were reversed to generate a decoy database that was concatenated to the original database. Related RNA-seq files have been deposited in the Sequence Read Archive database with accession SRA060572.

REANALYSED by: PAe005157

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Junmin Peng

LAB HEAD: Junmin Peng

PROVIDER: PXD000067 | Pride | 2013-08-28

REPOSITORIES: Pride

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U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.

Bai Bing B Hales Chadwick M CM Chen Ping-Chung PC Gozal Yair Y Dammer Eric B EB Fritz Jason J JJ Wang Xusheng X Xia Qiangwei Q Duong Duc M DM Street Craig C Cantero Gloria G Cheng Dongmei D Jones Drew R DR Wu Zhiping Z Li Yuxin Y Diner Ian I Heilman Craig J CJ Rees Howard D HD Wu Hao H Lin Li L Szulwach Keith E KE Gearing Marla M Mufson Elliott J EJ Bennett David A DA Montine Thomas J TJ Seyfried Nicholas T NT Wingo Thomas S TS Sun Yi E YE Jin Peng P Hanfelt John J Willcock Donna M DM Levey Allan A Lah James J JJ Peng Junmin J

Proceedings of the National Academy of Sciences of the United States of America 20130910 41

Deposition of insoluble protein aggregates is a hallmark of neurodegenerative diseases. The universal presence of β-amyloid and tau in Alzheimer's disease (AD) has facilitated advancement of the amyloid cascade and tau hypotheses that have dominated AD pathogenesis research and therapeutic development. However, the underlying etiology of the disease remains to be fully elucidated. Here we report a comprehensive study of the human brain-insoluble proteome in AD by mass spectrometry. We identify 4 ...[more]

PMID: 24023061

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	ad_a03.1.xml	Xml