MassIVE MSV000079531

Partial Public

GNPS Genomics Demo Submission

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Description

This is a demo GNPS-genomics submission, providing an example of a submission that is compatible with NRPquest / RiPPquest / Glycogenomics and other MS/MS-genomic tools that are becoming available at GNPS. MS/MS data should be uploaded as Peak List / Raw Spectrum as usual. Sequence data should be uploaded as "Sequence Databases" in fasta format. In addition, the user need to create an excel file described below, save it as "Tab Delimited Text (.txt)" with the name "metabolome_genome_link.txt", and upload it as "Supplementary Files". metabolome_genome_link.txt file should have a first row header "SpectrumFile SequenceFile" and then in each row, there should be a spectrum file and a sequence file that the spectrum file should be searched against. An example can be : SpectrumFile SequenceFile spectrum_1.mzXML sequence_1.fasta spectrum_2a.mzXML sequence_2.fasta spectrum_2b.mzXML sequence_2.fasta spectrum_3.mzXML sequence_3a.fasta spectrum_3.mzXML sequence_3b.fasta In this case, spectrum_1.mzXML gets searched against seqeunce_1.mzXML, spectrum_2a.mzXML and spectrum_2b.mzXML get searched against sequence_2.fasta, and spectrum_3.mzXML gets searched against both sequence_3a.fasta and sequence_3b.fasta. To avoid time-consuming sequence data uploads, the user also have the option to simply put refseq or genbank accession numbers instead of uploading a fasta file as "Sequence database". To do this, the user should enter "#RefSeq:" and "#GeneBank:" followed by RefSeq or GeneBank accession. For example both spectrum_albus.mzXML #RefSeq:GCF_000359525.1 and spectrum_albus.mzXML #GenBank:GCA_000359525.1 are valid entries, and they search spectrum_albus.mzXML against : http://www.ncbi.nlm.nih.gov/assembly/GCF_000359525.1/ Please see the demo dataset submission for more information. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Demo

Contact

Principal Investigators:
(in alphabetical order) 		Pavel Pevzner
Submitting User: hmohiman
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

GNPS content goes here (MSV000079531 [task=802bf8942ad7410a81bc4d3673f947e0])
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.