Description
LFQ benchmark from commercial digests according to
Kuharev, Joerg, et al. (2015)
Sample A 5%, 30%, 65% E.coli, Yeast, Human; 1ug on column
Sample B 20%, 15%, 65% E.coli, Yeast, Human; 0.7ug on column
Sample C Average of Sample A and B for Spectral Library by Gas-Phase Fractionationation; 1ug on column (just for completeness, I do not use GPF anymore for my applications, please use predicted libraries or use the GPF with caution).
The dilution of sample B to 70% of total concentration lifts up measured log2 fold-changes by +0.5. For non-normalized data, expected log2 fold-changes are -1.5 (E.coli), +0.5(Human), +1.5 (Yeast).
A perfect cross-run normalization would restore log2 fold-changes to the classical values of -2,0,+1. If a normalization does not perform as expected or over-corrects, this LFQ benchmark can show this especially on the precursor level.
30 min linear gradient on a classical nanflow trap-elute setup using Dionex3000 and Acclaim PepMap columns.
[doi:10.25345/C5CN6Z423]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: LFQ benchmark, Multi-Species Mixtures, Quantitative Accuracy
Contact
Principal Investigators:
(in alphabetical order)
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Andrej Shevchenko, MPI-CBG Dresden, Germany
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Tobias
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Conditions:
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Biological Replicates:
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Technical Replicates:
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| Identification Results |
Proteins (Human, Remapped):
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Proteins (Reported):
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Peptides:
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Variant Peptides:
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PSMs:
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Differential Proteins:
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Quantified Proteins:
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Click here to queue conversion of this dataset's submitted spectrum files
to open formats (e.g. mzML). This process may take some time.
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.