MassIVE MSV000083948

Partial Public PXD000427

Human substantia nigra proteome dataset

Description

Quantitative proteomic analysis of human post-mortem substantia nigra from patients with Parkinson’s disease (n=3) versus controls (n=3) based on sixplex TMT (TMT6) isobaric labeling which allowed protein simultaneous identification and quantification. Samples were digested and pooled after TMT6 labeling. Peptides were fractionated by OFFGEL electrophoresis (24 fractions). Each peptidic fraction was analyzed in two technical replicates by LC?MS/MS analysis on a LTQ Orbitrap XL mass spectrometer equipped with a NanoAcquity HPLC system. MS data were processed using EasyProtConv (v. 1.21). Peak lists were generated from raw data combining CID and HCD spectra, and submitted to Easyprot (v2.2) which uses Phenyx (GeneBio, Geneva, Switzerland) for protein identification [1]. Searches were conducted against UniProt Swiss-Prot database (08-Feb-2011, 525’207 entries) specifying Homo sapiens taxonomy. Trypsin was selected as the proteolytic enzyme, one missed cleavage was allowed, cysteines carbamidomethylation, TMT6 amino terminus and TMT6 lysine were set as a fixed modification whereas oxidized methionine as variable. The minimum peptide length was five amino acids and precursor error tolerance was 10 ppm. False positive ratios were estimated using a reverse decoy database [3]. Peptide z-scores were set to maintain a false positive peptide ratio below 1%. Proteins with at least two unique distinct peptide sequences were selected and clustered based on shared peptides indistinguishable by MS [4] using Isobar (v 1.3.1) package. The protein entry containing the most peptides was selected as the group reporter. For protein quantification, TMT6 reporter ion intensities were extracted, corrected for isotopic impurities as provided by the manufacturer and each channel was normalized imposing equal median intensity. Only spectra from protein specific peptides not eliminated after outlier filtering were used for quantification. Isobar R package (v 1.3.1.) was used to calculate protein ratios and select statistically significant differentially regulated proteins between the two states. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Human ; HPP brain ; substantia nigra ; post-mortem tissue ; Parkinson's disease ; OFFGEL LC/MS/MS Orbitrap

Contact

Principal Investigators: None Listed
Submitting User: ccms

Publications

Licker V, Turck N, Kövari E, Burkhardt K, Côte M, Surini-Demiri M, Lobrinus JA, Sanchez JC, Burkhard PR.
Proteomic analysis of human substantia nigra identifies novel candidates involved in Parkinson's disease pathogenesis.
Proteomics. 2014 Mar;14(6):784-94. Epub 2014 Feb 18.

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Experimental Design
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Identification Results
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Quantification Results
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.