MassIVE MSV000097608

Imported Reanalysis Dataset Public PXD047839

timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)

Subscribe Comment Add Reanalysis

Description

Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein quantitation across large patient cohorts. Here we demonstrate the qualitative and quantitative performance gain of the timsTOF HT over the timsTOF Pro 2 mass spectrometer in the analysis of neat (unfractionated) and Proteograph™ (PG)-processed plasma across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV<20%) with timsTOF HT compared to timsTOF Pro 2. In an exploratory study of 20 late-stage cancer and 20 control sampleswe observed a ~50% increase in total and statistically significant plasma peptide precursors (q<0.05) with timsTOF HT compared to Pro 2. Our data demonstrated the superior performance of timsTOF HT in identifying and quantifying differences between biologically diverse samples, which can improve disease biomarker discovery in large cohort studies. Moreover, researchers can leverage datasets from this study to optimize their LCMS workflows for plasma protein profiling and biomarker discovery. See the details in a paper, entitled "timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery". [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Plasma ; Liquid chromatography ; Mass spectrometry ; Timstof ; Proteomics ; Biomarkers ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Bruce Wilcox, PrognomiQ Inc., N/A
Submitting User: ccms
Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
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.