MassIVE Reanalysis - RMSV000000327.2

RPXD019844.2

MassIVE.quant reanalysis from offline PD+MSstatsTMT results

Description

The same PSM report from Proteome Discoverer 2.4.1.15 (Thermo Fisher Scientific) in RMSV000000327.3 was used for this reanalysis. For statistical analysis, data preprocessing, multiple fractions combination, data normalization with reference channel, protein summarization, and statistical testing using MSstatsTMT v1.6.2 was performed. The PSM report measures the training cohort described in the original manuscript, which includes 17 replicates from 17 Healthy patients, 19 replicates from 18 non-COVID-19 patients, 20 replicates from 18 non-severe COVID-19 patients and 14 replicates from 13 severe COVID-19 patients. The remaining 20 replicates are not used for this reanalysis and thus were labeled as "Empty" condition. R script for MSstatsTMT analysis is available in the 'methods' folder (FTP download -> methods). [doi:10.25345/C5TX55]

[See results attachment job for details]

Keywords: COVID-19 ; Proteomics ; Metabolomics ; Severity ; MassIVE.quant reviewed - Platinum ; CoronaMassKB ; ProteoCarta

Reanalyzed Datasets

  • MSV000085507 : GNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Number of Files: 18
Total Size: 42.98 GB
 
Experimental Design
    Conditions:
5
    Biological Replicates:
67
    Technical Replicates:
20
 
Quantification Results
    Differential Proteins:
339
    Quantified Proteins:
786
 
Browse Reanalysis Files
Browse Quantification Results Browse Metadata
 
FTP Download Link (click to copy):

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.