MassIVE Reanalysis - RMSV000000291.1

RPXD017628.1

ScottA-Qvalue : Quantification and differential abundance analysis by MSstats

Description

Proteomics experiment on Listeria monocytogenes strains ScottA was performed in biological triplicates (control, high osmolarity, low pH, bile), except for EGD-e bile, where we could only quantify duplicates. All Listeria data sets data were analyzed using Spectronaut v12 (Biognosys) using standard settings (dynamic peak detection, automatic precision nonlinear iRT calibration, interference correction, and cross run normalization). Results were filtered for a qvalue of 0.01 on the peptide level. Peptides for protein group quantitation were selected using Qvalue (only individual values passing the qvalue threshold of 0.01 were considered, NAs in data matrix) without imputation. MSstats v3.12 was used for differential abundance analysis. R script is available in the ‘methods’ folder. [doi:10.25345/C50X63]

[See results attachment job for details]

Keywords: MassIVE.quant reviewed - Platinum

Reanalyzed Datasets

  • MSV000083881 : A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships
Number of Files:
Total Size:
 
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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Browse Quantification Results Browse Metadata
 
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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.