MassIVE Reanalysis - RMSV000000253.1

MassIVE.Quant-Reanalysis-Skyline

Description

The dataset included 16 proteins in ten dilution steps into three different backgrounds(water, whole-cell protein extracts from human or yeast). We used the datasets with human cell protein extracts background. In Skyline (daily version 3.5.2.9703) a new document was created with default settings, plus heavy Lysine and Arginine with 13C and 15N labeling, and chromatogram extraction was set to use TOF extraction at 40,000 resolving power applying to all MS/MS spectra within a 25-m/z precursor isolation range around the 32-target m/z values used and 10 minutes of predicted retention times using the iRT library. The assay library file OpenSWATH_SM4_GoldStandardAssayLibrary.csv with all decoys removed was imported into Skyline using File > Import > Transition List, along with the iRT assay library, despite the fact that the library contains only 3 or 4 fragment ions per precursor. An equal number of pseudo-reversed sequence decoys were generated for mProphet model generation.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. **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/C57J06]

[See results attachment job for details]

Keywords: MassIVE.quant reviewed - Platinum

Reanalyzed Datasets

  • MSV000081829 : PASS00289 - OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data:SWATH-MS Gold Standard (SGS) Dataset, S. pyogenes Dataset
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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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.