MassIVE MSV000094137

Partial Public PXD049979

Proteome Profiling - Quality and Quantifiability using the Orbitrap Astral MS (IBD)

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Description

Biomarker development has two key challenges; the high rate of false positives in discovery and the slow validation phase. To address these challenges we have developed and rigorously tested the Targeted Evaluation and Assessment of Quality (TEAQ) software package. This innovative tool for identifying and selecting precursors, peptides, and proteins that meet the stringent criteria of targeted assays, thus overcoming the limitations faced in the current biomarker development landscape. We implemented the TEAQ to evaluate the performance of the Orbitrap Astral MS using Data-Independent Acquisition Mass Spectrometry (DIA-MS) on plasma samples. This assessment focused on crucial parameters such as proteome linearity, specificity, repeatability, reproducibility, and others essential for substituting dedicated targeted techniques in the more rigorous discovery phase of biomarker development. Through the application of TEAQ on a clinical cohort comprising individuals with inflammation bowel disease (n=493) and an 11-point loading curve, our software successfully identified the signature precursors of quantifiable proteins. A signature peptide or precursor, as per our definition, is a unique peptide or precursor sequence specific to the target protein, exhibiting no miss-cleavages, a linearity R2 value exceeding 0.8, and a coefficient of variation (CV) below 20%. Furthermore, deviations should be less than 20% at low limited quantification concentrations. In instances where multiple peptides or precursors originate from the same protein, it is imperative that all peptides demonstrate a correlation coefficient within the same proteins (>0.7) in the study. Our data set has been made available to as a resource for targeted assay development. This comprehensive approach ensures the reliability and accuracy of our biomarker identification process, paving the way for advancements in clinical practice. [doi:10.25345/C5PZ51X8N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Biomarker Identification ; DIA ; Orbitrap Astral ; Quality Control ; Proteome Profiling ; IBD

Contact

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

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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.

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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.