MassIVE Reanalysis - RMSV000000261.4

RPXD015096.4

MassIVE.Quant-Reanalysis-Proteome Discoverer

Description

MS/MS spectra were searched using Proteome Discovery software suite (v1.4) and Mascot (v2.5) as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precursor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. Peptide areas were extracted with the Precursor Area Ion Detector module of Proteome Discoverer with a mass tolerance of 2 ppm. The report for PSM level is used for downstream statistical analysis. The differential abundance analysis was performed by MSstats (v3.13.5) 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/C5643W]

[See results attachment job for details]

Keywords: MassIVE.quant reviewed - Platinum

Reanalyzed Datasets

  • MSV000084181 : MSstats splitplot method for protein quantitation in MS datasets
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:
 
Browse Reanalysis Files
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.