MassIVE Reanalysis - RMSV000000308.3

Differential analysis using MSstatsTMT and limma

Description

Raw data were analyzed with Maestro and the PSM file was exported to R for the downstream statistical analysis. Data processing, protein quantification, and normalization steps were performed using MSstatsTMT v2.2.0. In total, 2,604 proteins were quantified and used for statistical analysis. Various statistical approaches, including MSstatsTMT and limma, are applied to detect changes in abundance In order to see how the unbalanced design impacted the performance of differential analysis, we manually generated an unbalanced design by eliminating a subset of samples from each mixture. [doi:10.25345/C51Z41X9V]

[See results attachment job for details]

Keywords: SARS-CoV-2 ; translatome ; proteome

Reanalyzed Datasets

  • MSV000085096 : Proteome and Translatome of SARS-CoV-2 infected cells
Number of Files: 33
Total Size: 179.11 MB
 
Experimental Design
    Conditions:
9
    Biological Replicates:
3
    Technical Replicates:
2
 
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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.