MassIVE MSV000095742

Partial Public PXD055481

QCeltis Case Study 1: Depleted Plasma QC Dataset

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Description

A dataset containing depleted plasma samples used as quality control technical replicates (TR) and digestion replicates (DR). Plasma aliquot was shunted to Top14 Abundant Protein Depletion Resin (A36372) based depletion. Depleted plasma samples were processed on a i7 automated liquid handling system (Beckman Coulter) in a 96-well plate for protein denaturation, cysteine reduction and alkylation, and trypsin digestion. Healthy control pooled samples were used as DRs and embedded between samples during digestion. Depleted plasma tryptic peptides were separated by EVOSEP One LC System (Evosep) over a 45-minute gradient injected into an Orbitrap Exploris 480 MS (Thermo Fisher) using DIA-MS settings as described by McArdle and Binek et. al. During MS acquisition, the 4 DRs are run at the beginning of each batch. In addition, pooled, bulk digested plasma samples from Parkinsons Disease patients are included as technical replicates (TRs) at the beginning and middle of every MS batch, with the goal of assessing LC-MS performance. [doi:10.25345/C52Z1318Q] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Quality Control ; DIA ; Digestion Replicates ; Technical Replicates ; Depleted Plasma

Contact

Principal Investigators:
(in alphabetical order) 		Jennifer Van Eyk, Cedars Sinai Medical Center, United States
Submitting User: vegesnam

Publications

Vegesna M, Sundararaman N, Bharadwaj A, Washington K, Pandey R, Haghani A, Chazarin B, Binek A, Fu Q, Cheng S, Herrington D, Van Eyk JE.
Enhancing Proteomics Quality Control: Insights from the Visualization Tool QCeltis.
J Proteome Res. 2025 Mar 7;24(3):1148-1160. Epub 2025 Feb 24.

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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.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) 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 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.