MassIVE MSV000080697

Imported Reanalysis Dataset Public PXD003215

A Novel Method for Isolating Whole Protein from Human Cranial Bone

Subscribe Comment Convert Spectra Reanalyze Spectra Add Reanalysis

Description

The presence of the extracellular matrix within human bone limits the applicability of conventional protocols for protein extraction. As a result, complete and accurate characterization of human bone proteome is yet to be performed, and as a result, several bone-related diseases such as craniosynostosis and osteosarcoma are still poorly understood. We sought to develop a reproducible method for extracting whole proteins of varying molecular weights from human cranial bone. Whole protein was extracted from human cranial suture by mechanically processing samples using a method that minimized heat introduction to proteins to limit degradation. Western blotting suggests the presence of whole protein while mass spectrometry was used to sequence peptides and identify isolated proteins. Molecular weights of extracted protein ranged from 9.4-629 kDa and contained proteins of both intra- and extra-cellular origin. High correlation scores among suture protein spectral counts suggest the reproducibility of the method. Ontology analytics revealed proteins of myriad functions including mediators of metabolic processes and cell organelles. These results suggest a reproducible method for isolation of whole protein representing a large range of molecular weights, origins and functions. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Q-Exactive ; Protein ; Extraction ; Human ; Method ; Whole Protein ; Cranial Bone ; Proteome

Contact

Principal Investigators:
(in alphabetical order) 		Dr. Russell R. Reid, MD, PhD, The Laboratory of Craniofacial Development and Biology, Section of Plastic and Reconstructive Surgery, University of Chicago Medicine, N/A
Submitting User: ccms

Publications

Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR.
A method for whole protein isolation from human cranial bone.
Anal. Biochem. Epub 2016 Sep 25.

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.