MassIVE Reanalysis - RMSV000000251.1

RPXD014101.1

MassIVE.Quant-Reanalysis-Skyline-lowCV

Description

Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup). Importing the forward and reversed FASTA file resulted in targets for 4246 proteins, 58,168 peptides, 74,314 precursors, and 445,884 fragment ions, at 4.5% protein, 0.34% unique peptide FDR by reversed sequence decoy counting. Reversed sequences, accounting for 193 proteins and 200 peptides, were left in the targets list to be carried through the subsequent “Reproducibility” experiment. An equal number of shuffled sequence decoys were generated for mProphet model generation. The runs (n = 8 – reported as n = 4 in the paper) acquired for the “Reproducibility” experiment were then imported into the template, an mProphet model trained and applied. Next, the targets were filtered for peptides detected at q value less than 0.01 in at least 4 (of 8) runs, and where the CV of the detected peak areas, median normalized, was less than 20%, resulting in targets for 2212 proteins, 13,744 peptides, 18,910 precursors, and 113,460 fragment ions, at 1% protein, 0.18% unique peptide FDR by reversed sequence decoy counting. The remaining peptides comprised 249 of 2367 –10.5% – Oxidation (M), 679 of 18,479 – 3.7% – unmodified semi-tryptic, and 12,816 of 37,322 – 34.3% – unmodified tryptic peptides. As expected, Oxidation (M) and semi-tryptic peptides made it through this filter at much lower rates than unmodified fully tryptic peptides. An equal number of shuffled sequence decoys of matching types were generated for mProphet model generation. The 18 runs were then imported into the template an mProphet model trained and applied. The MSstats report was exported for further analysis. The differential abundance analysis was performed by MSstats (v3.16.0) R package. Details for data processing and statistical analysis are available in description.pdf ('Methods' folder). **Publication : Choi et al. (Under revision) MSstats increases the reproducibility of detecting differentially abundant proteins across tools that process raw mass spectra. [doi:10.25345/C54Q7N]

[See results attachment job for details]

Keywords: MassIVE.quant reviewed - Platinum

Reanalyzed Datasets

  • MSV000081677 : SWATH Analysis of Yeast Proteome over Time in Response to Osmotic Stress
Number of Files:
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Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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Species

Instrument

Modifications
Number of distinct conditions analyzed in this reanalysis.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates in this reanalysis.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates in this reanalysis.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed in 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 in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported in this reanalysis.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified in this reanalysis.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison in this reanalysis.

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 reanalysis.

"N/A" means no results of this type were submitted.