MassIVE Reanalysis - RMSV000000258.5

MassIVE.Quant-Reanalysis-Spectronaut-top3 features

Description

A spectral library was generated using all available raw files (24 DDA files plus 24 DIA files) using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. Data processing was performed as described in the original manuscript. The uniprot human reference proteome from 2017.06.14 was used for the spectrum centric data analysis for library generation. Further included were the custom FASTA file for the spike-in proteins as well as the MaxQuant contaminants FASTA file. The resulting library was further filtered to remove all overlapping peptide sequences between the human background proteome and the spike-in proteins. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema. Quantification result is the same as in RMSV000000252.2. The differential abundance analysis was performed by MSstats (v3.16.2) R package: Top 3 features were used for this reanalysis. Details for data processing and statistical analysis are available in description.pdf. **Publication : Tsai TH, Choi M, Banfai B, Liu Y, MacLean BX, Dunkley T, Vitek O. (2020). Selection of features with consistent proles improves relative protein quantification in mass spectrometry experiments. Molecular & Cellular Proteomics. 2020 March 31, 19(6) 944-959, doi:10.1074/mcp.RA119.001792. PMID: 32234965. [doi:10.25345/C55B1W]

[See results attachment job for details]

Keywords: MassIVE.quant reviewed - Platinum

Reanalyzed Datasets

  • MSV000081828 : PASS00589 - Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues
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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.