MassIVE Reanalysis - RMSV000000258.2

MassIVE.Quant-Reanalysis-Skyline-top5 features

Description

In Skyline (version 3.7.0.11317) a new document was created with default settings, plus Oxidation (M), Acetyl (N-Term), Amonia Loss (K, N, Q, R), and Water Loss (D, E, S, T) modifications, precursor charge states 1-7 and fragment charge states 1-6, for fragment types y, b and precursor, the 6 most intense library fragment ions and chromatogram extraction was set to use 15 ppm mass tolerance applying to all centroided MS/MS spectra using the 19 variable window isolation schemed defined in the paper, with 1 m/z margins, spanning 400-1220 m/z and 10 minutes of predicted retention times using the iRT values found in the paper assay library. Quantification result is the same as in RMSV000000252.1. The differential abundance analysis was performed by MSstats (v3.16.2) R package: Top 5 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/C5JH92]

[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
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.