MassIVE MSV000078539

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iPRG 2009: Differential proteomics in Orbitrap E. coli lysates

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Description

The files in directory were generated as part of the ABRF iPRG 2009 Study. The sample is E. coli lysate. The five "red" RPLC runs lack the "green" set of proteins. The five "yellow" runs lack the "blue" set of proteins. Both red and yellow runs contain a spike of BSA to enable quantitative comparison among runs. Proteins were reduced and alkylated by DTT and iodoacetamide, respectively, and separated in a 1D gel. The proteins were trypsinized, and the peptides were added to the in-solution digest of BSA. In a collaboration between the Ayers Institute and Mass Spectrometry Research Center at Vanderbilt University Medical Center, the red and yellow samples were each separated five times in an RPLC/MS/MS experiment lasting 184 minutes (of which the shallow gradient lasted two hours ). The instrument collecting data was a Thermo LTQ-XL Orbitrap. Eight centroided tandem mass spectra were collected following each profile MS scan. Collection of these data was supported by U24 CA126479. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: N/A

Contact

Principal Investigators:
(in alphabetical order) 		David L. Tabb
Submitting User: dtabb73

Publications

Brian C. Searle, David L. Tabb, Sean L. Seymour, Paul A Rudnick, et al.
ABRF iPRG 2009 Study: Testing for Differences Between Complex Samples in Proteomics Datasets.
https://abrf.org/wp-content/uploads/iprg2009_presentation.pdf.

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Experimental Design
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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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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.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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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.