MassIVE MSV000083710

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Simply extending the EThcD MS/MS range increases the confidence in N-glycopeptide identification.

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Description

Glycoproteomics raw files containing all classes of N-glycopeptides. Each file has been run as HCD-pd-EThcD where EThcD was triggered upon observation of signature glycopeptide oxonium ions. Additionally each file was measured with 2 different m/z ranges; standard (up to 2000 m/z for both HCD and EThcD) and extended (up to 4000 m/z for HCD and EThcD). CHOKO_FT_IMAC_SAX denotes SAX enriched glycopeptides from CHO cells containing mainly complex multiply sialylated N-glycopeptides. CHOKO_IMAC contains glycopeptides modifed with mannose-6-phosphate. TestGly refers to human milk glycopeptides that contain complex type N-glycopeptides with multiple fucose residues. [doi:10.25345/C5GS62] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: EThcD ; Glycoproteomics

Contact

Principal Investigators:
(in alphabetical order) 		Albert J.R. Heck, University of Utrecht, Netherlands
Submitting User: TCaval
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Experimental Design
    Conditions:
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Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
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Quantification Results
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    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.