MassIVE MSV000091290

Complete Public PXD040129

Bone collagen from South African rodent species identification using Zooarchaeology by Mass Spectrometry (ZooMS)

Subscribe Comment Reanalyze Spectra Compare Results Add Reanalysis

Description

The dataset is for identification of MALDI markers for peptide mass fingerprinting of bone collagen for species identification using ZooMS. Corresponding MALDI data can be found through Zenodo at [ADD]. This dataset contatins: - raw files - peak list files - results files final confirmation biomarker searches - databases for the whole proteome, de novo marker development, and confirmation biomarker searches - csv file with information about the sample number [doi:10.25345/C53T9DG9Q] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: archaeology ; bone ; collagen ; ZooMS ; South Africa ; rodent

Contact

Principal Investigators:
(in alphabetical order) 		Carli Peters, Max Planck Institute of the Science of Human History, Germany
Katerina Douka, University of Vienna, Austria
Kristine Korzow Richter, Max Planck Institute for the Science of Human History, Germany
Submitting User: kkrichter

Publications

Hillestad Nel T, Peters C, Korzow Richter K, Henshilwood C, van Niekerk K, Douka K.
Peptide mass fingerprinting as a tool to assess micromammal biodiversity in Pleistocene South Africa: The case of Klipdrift Shelter.
Quat. Sci. Rev. 2023 Dec; 322; 108380. doi: 10.1016/j.quascirev.2023.108380.

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 Browse Results
Browse Metadata
 
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.