MassIVE MSV000090837

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DIA_staggered_LFQ_Benchmark_High-Performance_QE-HF_30,90,150minGradient

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Description

LFQ Benchmark with samples from commercial digests according to Kuharev, Joerg, et al (2015). Sample A: 5% E.coli, 30 % Yeast, 65% Human, 0.9ug on column. Sample B: 20% E.coli, 15% Yeast, 65% Human, 0.9ug on column. (4 replicates per gradient length, one aliquot per 4 samples from one mastermix per sample type). Expected log2 fold-changes of -2,0,+1 for E.coli, Human, Yeast. Sample C: 0.9ug on column, average of A and B used to build enhanced spectral library by Gas-Phase-Fractionation. Sample C files are here for completeness, obtained libraries can lead to improvements but I do not use refined libraries for my applications anymore, use at own caution and risk. Notably, the chromatography was performed with uPAC analytical column, resulting in sharp and symmetric <20s short chromatograms. Gradients (30,90,150 min) were 2-sloped and linear, with the last third of the gradient encompassing half of the %B increase. Analysis with Spectronaut might not be ideal as MS1 was recorded at 30k resolution. This dataset, in particular the 90min gradient ones, can possibly lead to the strongest LFQ benchmark results and might serve as upper standards in comparisons. [doi:10.25345/C5QZ22N56] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: LFQ, DIA, Benchmark, Accuracy, Multi-Species Mixture

Contact

Principal Investigators:
(in alphabetical order) 		Andrej Shevchenko, MPI-CBG Dresden, Germany
Submitting User: Tobias
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Experimental Design
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Identification Results
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Quantification 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.

"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.

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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.