MassIVE MSV000100428

Partial Public PXD072865

AX4 PPK1 Insoluble Dictyostelium proteomics, Scaglione Lab Duke

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Description

Quantitative LC/MS/MS was performed on 2 uL of each sample, using a Vanquish Neo UPLC system (Thermo) coupled to a Thermo Orbitrap Astral high resolution accurate mass tandem mass spectrometer (Thermo). Briefly, the sample was first trapped on a Symmetry C18 20 mm x 180 um trapping column (5 ul/min at 99.9/0.1 v/v water/acetonitrile), after which the analytical separation was performed using a 1.5 um EvoSep 150um ID x 8cm performance (EvoSep) column with a 30 min gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 500 nanoliters/minute (nL/min) with a column temperature of 50C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (m/z 200) full MS scan from m/z 380-980 with a target AGC value of 4e5 ions. Fixed DIA windows of 4 m/z from m/z 380 to 980 DIA MS/MS scans were acquired in the Astral with a target AGC value of 5e4 and max fill time of 6 ms. HCD collision energy setting of 27% was used for all MS2 scans. [doi:10.25345/C56W96P44] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: label free, proteomics ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Matthew Scaglione, Duke University, USA
Submitting User: es3064
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

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

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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.