MassIVE MSV000082867

Imported Reanalysis Dataset Public PXD005921

Early-stage cancer biomarkers uncovered in the blood platelet proteome

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

Platelets play an important role in tumor growth and at the same time, platelet characteristics are affected by cancer presence. Therefore, we investigated whether the platelet proteome can be used as a source for biomarkers of early-stage cancer. Patients with early-stage lung (n=8) and head of pancreas cancer (n=4) were included, as were healthy sex- and age-matched controls for each subgroup. Blood samples were collected from controls and from patients before surgery. Furthermore, from six of the patients, a second sample was collected two months after surgery. NanoLC-MS/MS-based proteomics was used to quantify and compare the platelet proteome of patients to controls. Also, samples before surgery and after surgery were compared. Analysis revealed that the platelet proteome of patients with early-stage cancer is altered as compared to controls. In addition, the platelet proteome changed after tumor resection. Using the above data, in conjunction with quantitative filtering, we were able to select seven potential platelet-derived biomarkers of early-stage cancer. This pioneering study on the platelet proteome in cancer patients clearly identifies platelets as a new source of protein biomarkers of early-stage cancer. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Human ; platelets ; label-free ; lung cancer ; pancreatic cancer ; biomarkers

Contact

Principal Investigators:
(in alphabetical order) 		Connie Ramona Jimenez, OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands, N/A
Submitting User: ccms

Publications

Sabrkhany S, Kuijpers MJE, Knol JC, Olde Damink SWM, Dingemans AC, Verheul HM, Piersma SR, Pham TV, Griffioen AW, Oude Egbrink MGA, Jimenez CR.
Exploration of the platelet proteome in patients with early-stage cancer.
J Proteomics. Epub 2018 Mar 10.

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.