MassIVE MSV000099243

Partial Public PXD068610

Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood

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Description

Mitra devices were used to capture 20 uL of whole blood (heparin or EDTA) followed by extraction with 5% deoxycholate (SDC) in ammonium bicarbonate, reduction/alkylation and digestion for 2 h with TPCK-trypsin. SDC was precipitated with acid and filtered. Peptides were adjusted to 80% MeCN and 1% TFA followed by purification of N-glycopeptides using Polyhydroxyethyl A spin tips. The flow though was saved for phosphopeptide enrichment, and N-glycopeptides were eluted with 0.1% TFA. Phosphopeptides were enriched using Ti-IMAC after adjusting 300 uL of flow through to 5% TFA and 0.25 M glycolic acid, and phosphopeptides were eluted with 1% NH4OH. The unenriched digest was analyzed by microflow LC and data-independent acquisition. The N-glycoenriched fraction was analyzed using an Evosep LC and Orbitral stepped-collision energy DDA-MS/MS or Orbitrap Astral DIA-MS/MS. Analyses used Spectronaut, GlycoDecipher and FragPipe glyco-N-DIA workflow with visualization in Skyline. Other details are given in the metadata file. [doi:10.25345/C5WM1466D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: n-glycoproteome ; mitra device ; sepsis ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Matthew W. Foster, Duke University, USA
Submitting User: mwfoster
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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.

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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.

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