MassIVE MSV000094508

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EVs enriched from plasma by placental proteins

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Description

Plasma EVs were enriched using placental protein markers. The proteins were extracted in 5% SDS and processed with S-Trap 96 well plates without reduction and alkylation to preserve potential labile PTMs. Digestion was performed with trypsin. Eluted peptides were loaded onto EvoTips and peptides were analyzed using an EvoSep one with a 30SPD method (15cm column and approximately 44 minutes of run time) coupled to a TIMSTOF Flex mass spectrometer with 20um CaptiveSpray emitter. A default diaPASEF method in TIMSControl 5.0 was used "Short gradient diaPASEF" with the exception that the upper 1/k0 limit was increased to 1.45 for MS1 to allow the monitoring of the 1222 internal calibrant during run times. This is essential as the Johns Hopkins University does not have buildings with functional HVAC and calibrations can drift considerably during all run times. Monitoring the 1222 ion mass and ion mobility every 4 hours is required to identify when instrument calibrations are required, on average every 8-12 hours. [doi:10.25345/C5RX93Q92] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Placenta plasma EVs ; Plasma proteomics ; Human pregnancy proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Benjamin Orsburn, Johns Hopkins, United States
Submitting User: ben_orsburn
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Identification Results
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Quantification Results
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Number of distinct biological 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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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.