MassIVE MSV000085932

Complete Public PXD020801

HUPO HPP Phosphopeptide Challenge

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Description

The Phosphopeptide Challenge of the MS Resource Pillar of the Human Proteome Project (HPP) provides a unique opportunity for the HUPO membership to evaluate and compare methods for peptide sequence analysis by mass spectrometry, phosphosite localization, phosphopeptide enrichment, and data processing. Each participant is to apply their own methods and chosen bioinformatic pipeline to fully characterize the provided Phosphopeptide Challenge samples. As a result of this collaborative endeavor, multiple purification schemes, analytical protocols and data processing strategies will be evaluated, making it possible to determine the approach(es) that provide the highest coverage of the phosphopeptides in the mixture. Each participating laboratory will receive two sample vials. The vial labeled 'Phosphopeptide' contains a set of synthesized phosphorylated (Ser, Thr, or Tyr) peptides of human sequence origin at various concentrations, mixed with their non-phosphorylated counterparts. For some peptides, there is more than one phosphorylated form. The peptide sequences are included in the attached Excel file. The second vial labeled 'Phosphopeptide-Yeast' contains the same peptides in a background matrix consisting of 6 ug of trypsin-digested yeast lysate. Each vial is provided dry. Resuspension in 100 uL will result in synthetic peptide concentrations of 3 fmol/uL to 30 fmol/uL. The goal for the study is for you to provide your best method(s) to: 1. Identify the peptide sequences in the vial and determine the number and location of phosphorylation sites on each peptide (Phosphopeptide). 2. Determine the relative abundance of phosphorylation at each modified site by comparison with its non-phosphorylated counterpart (Phosphopeptide). 3. Enrich for phosphorylated peptides from the sample containing the yeast background matrix and re-analyze by MS (Phosphopeptide-Yeast). [doi:10.25345/C5BJ38] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: HUPO ; HPP ; Phosphopeptide ; Challenge ; Phosphorylated peptides ; phospho site localization ; phosphopeptide enrichment ; false identification rate ; Human Proteome Project ; mass spectrometry

Contact

Principal Investigators:
(in alphabetical order) 		Michael Hoopmann, Institute for Systems Biology, United States
Robert L. Moritz, Institute for Systems Biology, United States
Susan Weintraub, UT Health San Antonio, USA
Ulrike Kusebauch, Institute for Systems Biology, United States
Submitting User: hpp_ppep_2018
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Experimental Design
    Conditions:
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Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
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.