MassIVE MSV000086696

Partial Public PXD023607

Top-down proteomic analysis with FAIMS of Alzheimer's disease derived brain tissue

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Description

Proteomic datasets collected from a single human midfrontal cortex tissue sample. Tissue was homogenized in 8 M Urea, 10 mM ABC, and 10 mM TCEP before subsequent cleanup with 100K and 3K MWCO filters. NanoLC was performed for RP separation. Three technical replicates were collected without FAIMS. Seven FAIMS compensation voltages with three technical replicates each were also collected, for a total of 21 FAIMS datasets. Raw files were collected in "full-profile" mode on a Thermo Fusion Lumos mass spectrometer. Data was searched with TopPIC v1.3 using PNNL's DMS processing pipeline. [doi:10.25345/C5WN4N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: top-down ; FAIMS ; Alzheimer's ; cortex

Contact

Principal Investigators:
(in alphabetical order) 		Vladislav A. Petyuk, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Fulcher JM, Makaju A, Moore RJ, Zhou M, Bennett DA, De Jager PL, Qian WJ, Pasa-Tolic L, Petyuk VA.
Enhancing Top-Down Proteomics of Brain Tissue with FAIMS.
J Proteome Res. Epub 2021 Apr 15.

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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.

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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.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.