MassIVE Reanalysis - RMSV000000281.1

RPXD017560.1

DIA : MP-LFC-MS1var-OT dataset, Spectronaut Pulsar X

Description

DIA data were analyzed with Spectronaut Pulsar X 12.0.20491.6, (Biognosys, Schlieren, Switzerland). The default settings were used for the targeted analysis of DIA data in Spectronaut. The initial mass tolerance for MS1 and MS2 was 15ppm. High precision iRT calibration was used. The analysis was performed with and without the built-in interference correction. The DDA spectra were analyzed with the MaxQuant (Version 1.5.6.5) analysis software using default settings (Trypsin/P, two missed cleavages). The search criteria included carbamidomethylation of cysteine as a fixed modification, oxidation of methionine and acetyl (protein N- terminus) as variable modifications. The initial mass tolerance for the precursor was 4.5 ppm and for the fragment ions was 20 ppm. The MP-LFC-MS1var-OT dataset was analyzed with Spectronaut Pulsar X using default settings using the spectral libraries from Bruderer et al. This dataset was normalized based on housekeeping proteins using a global median approach for MS1 and MS2 separately. Shared peptides between the proteomes were removed. Next, Precursor and protein False Discovery Rate were set to 1%. Since the detection limit of MS1 signal was around 100, normalized MS1 intensities below 100 were considered as missing values. Precursors with any missing MS1 intensities or MS2 intensities over all the MS runs were filtered out. The R scripts for statistical analysis were available in 'methods' folder. 6 raw files from MSV000084874 were used additionally. (File names are available in annotation.csv) [doi:10.25345/C5QM88]

[See results attachment job for details]

Keywords: MassIVE.quant reviewed - Platinum

Reanalyzed Datasets

  • MSV000084864 : Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition
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.