MassIVE MSV000079117

Partial Public PXD002114

ABRF PRG 2012: Longitudinal QC in Routine Peptide LC-MS/MS Analyses

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Description

Questions concerning data quality and reproducibility of proteomic laboratories spurred the ABRF-PRG group to design a study to systematically assess the reproducibility of proteomic laboratories. Sixty four participants were recruited from the broader mass spectrometry community and were asked to analyse provided aliquots of a digested 6 bovine protein mixture every month for a period of nine months. Data were uploaded to a central repository and the operators answered an accompanying survey. Forty five laboratories submitted a minimum of 8 data-dependent acquired LC-MSMS raw files No standard operating procedures were enforced; rather the participants were encouraged to analyse the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration; but rather to assess the temporal intra-laboratory reproducibility. The outcome of the study was reassuring in that 80% of the contributing laboratories were performing analyses at a medium to high level of reproducibility and quality. For the groups that had one to several outlying data sets, the major contributing factor that was correlated via the survey data was the preponderance of a preventative maintenance prior to the LC-MSMS analyses. Thus suggesting that laboratories should closely scrutinise the quality control data following such events. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: quality control ; longitudinal ; defined mixture ; multi-platform

Contact

Principal Investigators:
(in alphabetical order) 		Maureen Bunger
Submitting User: dtabb73
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Identification Results
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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.

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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.

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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.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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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.

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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.