MassIVE MSV000100019

Partial Public PXD071206

Input files: A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

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Description

Characterizing tumor-specific neoantigen peptides, which are derived from genomic or transcriptomic aberrations and presented to the immune system, is essential for studies in immuno-oncology. To facilitate this process, the modular iPepGen immunopeptidogenomics pipeline offers several key functions: (1) Neoantigen prediction and generation of a protein database from genomic or transcriptomic sequencing data; (2) Peptide identification; (3) Verification using immunopeptidomic mass spectral data; (4) Neoantigen classification and visualization; and (5) Candidate prioritization for further research. The pipeline is easily accessible through a publicly available, scalable cloud-based gateway and includes online interactive training materials. This streamlines adoption by cancer researchers, particularly those who may lack advanced computational expertise and resources for immunopeptidogenomic analysis. [doi:10.25345/C5XK8539J] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Neoantigen, immunopeptidomics, immuno-oncology, mass spectrometry, next generation sequencing, multi-omics, Galaxy, bioinformatics, workflow ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Timothy J.Griffin, University of Minnesota, United States
Submitting User: smehta
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Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
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Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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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.