MassIVE MSV000085763

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Blood to plasma processing : centrifugation

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Description

This dataset contains raw mass spectrometry data (in the form of Thermo Fisher .RAW files) supporting associated publication “Variable blood processing procedures contribute to plasma proteomic variability” by Halvey et al. The experiments characterized by these data evaluated effects on human plasma proteome of the following centrifugation parameters: number of spins (1 or 2), brake application (brake or no brake) and the speed of spin (1000g or 2000g). Conditions 1 through 8 correspond to following combinations of these factors - Condition 1: 1 spin 1000g no brake; Condition 2: 1 spin 1000g brake; Condition 3: 2 spins 1000g no brake; Condition 4: 2 spins 1000g brake; Condition 5: 1 spin 2000g no brake; Condition 6: 1 spin 2000g brake; Condition 7: 2 spins 2000g no brake; Condition 8: 2 spins 2000g brake. For the experiments investigating Conditions 1 and 4 there were several instances of LC-MS/MS analytical replicates for each individual sample. It should be noted that for these two experiments the corresponding .RAW files from the “./updates/2020-08-03_vfarutin_3259f343/raw/” folder under this dataset FTP address represent the actual LC-MS/MS runs used to generate the data in the associated paper by Halvey et al. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: blood ; plasma ; centrifugation

Contact

Principal Investigators:
(in alphabetical order) 		Anthony M. Manning, Momenta Pharmaceuticals, Inc., USA
Submitting User: vfarutin

Publications

Halvey P, Farutin V, Koppes L, Gunay NS, Pappas DA, Manning AM, Capila I.
Variable blood processing procedures contribute to plasma proteomic variability.
Clin Proteomics. 2021 Jan 19;18(1):5. Epub 2021 Jan 19.

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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.

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

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

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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