Dataset DOI: 10.5061/dryad.c2fqz61pc

Description of the data and file structure

Files and variables

This dataset is showing all proteins identified in indicated group of samples, combined by genotype/group.

Files (data generated at UCI, US):

• protDDA_Rd10_DR.csv

• protDDA_Rd10_CLR.csv

• protDDA_P23H.csv

• protDDA_RPE65_KO.csv

  Variables:

• P23H_het_M - heterozygous mice for P23H mutation in Rhodopsin, Male

• P23H_het_F - heterozygous mice for P23H mutation in Rhodopsin, Female

• Rd10_M - A mouse genotype with a point mutation in the Pde6b gene, leading to progressive photoreceptor (especially rod) degeneration, used as a model for retinitis pigmentosa, Male

• Rd10_F - A mouse genotype with a point mutation in the Pde6b gene, leading to progressive photoreceptor (especially rod) degeneration, used as a model for retinitis pigmentosa, Female

• Rd10_M_DR - A mouse genotype with a point mutation in the Pde6b gene, leading to progressive photoreceptor (especially rod) degeneration, used as a model for retinitis pigmentosa, Male, Dark Reared

• Rd10_F_DR - A mouse genotype with a point mutation in the Pde6b gene, leading to progressive photoreceptor (especially rod) degeneration, used as a model for retinitis pigmentosa, Female, Dark Reared

• RPE65_M - Mice lack functional RPE65, leading to impaired visual cycle, absence of 11-cis-retinal, and progressive retinal degeneration, Male

• RPE65_F - Mice lack functional RPE65, leading to impaired visual cycle, absence of 11-cis-retinal, and progressive retinal degeneration, Female

• WT_M - wild type mice, Male

• WT_F - wild type mice, Female

• Razor...unique.peptides

  Number of peptides used for quantification: unique to the protein or shared with a minimal number of proteins ("razor" peptides).

• Unique.peptides

  Number of peptides that are unique to a single protein group (not shared with others).

• Sequence.coverage....

  Percentage of the protein sequence covered by all identified peptides.

• Unique...razor.sequence.coverage....

  Sequence coverage based only on unique and razor peptides.

• Unique.sequence.coverage....

  Sequence coverage based only on unique peptides.

• Mol..weight..kDa.

  Molecular weight of the protein in kilodaltons (kDa).

• Q.value

  Adjusted p-value (false discovery rate); measures the confidence of protein/peptide identification.

• Score

  A scoring value indicating the quality or confidence of peptide/protein identification (algorithm-dependent).

• Intensity

  Total signal intensity of the peptides matched to a protein; often used for quantification.

• iBAQ.peptides

  Number of theoretically observable peptides used in iBAQ (intensity-Based Absolute Quantification) calculation.

• MS.MS.count

  Number of tandem MS (MS/MS) spectra that have been assigned to peptides from the protein — indicates identification confidence.

• Protein.IDs

  List of all protein identifiers (e.g., UniProt IDs) associated with a protein group detected in the experiment.

• Majority.protein.IDs

  The main (majority) protein ID(s) among the group — used as a representative identifier for the protein group.

• Protein.names

  Common or descriptive names of the proteins (from databases like UniProt).

• Gene.names

  Standard gene symbols corresponding to the proteins (e.g., ACTB, GAPDH).

• WT_vs_P23H_logFC

  Log₂ fold change of protein abundance between two conditions — here, wild-type (WT) vs. P23H (likely a disease model or mutant). Positive = upregulated in P23H; negative = downregulated.

• id

  Unique identifier for each row (protein group) in the dataset, usually automatically generated by the analysis software.

Files: data generated at UEF, Finland

• protDIA_Rd10_DR.csv

• protDIA_P23H.csv

  Variables

• P23H_het_M - heterozygous mice for P23H mutation in Rhodopsin, Male

• P23H_het_F - heterozygous mice for P23H mutation in Rhodopsin, Female

• Rd10_M_DR - A mouse genotype with a point mutation in the Pde6b gene, leading to progressive photoreceptor (especially rod) degeneration, used as a model for retinitis pigmentosa, Male, Dark Reared

• Rd10_F_DR - A mouse genotype with a point mutation in the Pde6b gene, leading to progressive photoreceptor (especially rod) degeneration, used as a model for retinitis pigmentosa, Female, Dark Reared

• WT_M - wild type mice, Male

• WT_F - wild type mice, Female

  Statistical comparison columns: 

• WT_vs_(GENOTYPE)_AveExpr

  Average expression level of the protein across all samples (usually log₂-transformed intensity).

• WT_vs_(GENOTYPE)_t

  t-statistic from differential expression analysis between WT and P23H groups — reflects the strength and direction of change.

• WT_vs_(GENOTYPE)_P.Value

  Raw p-value indicating the probability that the observed difference is due to chance.

• WT_vs_(GENOTYPE)_adj.P.Val

  Adjusted p-value (e.g., FDR) correcting for multiple testing — used to assess significance more reliably.

• WT_vs_(GENOTYPE)_B

  B-statistic or log-odds that a protein is differentially expressed (higher = more likely DE); used in limma-based analyses.

• WT_vs_(GENOTYPE)_-log(P.Value)

  Negative log₁₀ of the p-value — larger values indicate stronger statistical significance (e.g., for volcano plots).

• WT_vs_(GENOTYPE)_-log(adj.P.Val)

  Negative log₁₀ of the adjusted p-value — used similarly to emphasize significance after correction.

  Protein information columns:

• Protein.Group

  Identifier for a group of proteins that cannot be distinguished based on peptides (typically grouped by shared peptides).

• Protein.Ids

  UniProt or database accession numbers for proteins in the group.

• Protein.Names

  Common or descriptive names of the proteins in the group.

• Genes

  Gene symbols associated with the proteins (e.g., RHO, GAPDH).

• WT_vs_(GENOTYPE)_logFC

  Log₂ fold change in protein abundance between (GENOTYPE) and WT.

  Positive = higher in (GENOTYPE)

  Negative = lower in (GENOTYPE)

• First.Protein.Description

  Detailed description of the first (or main) protein in the group — includes functional annotation, organism, etc.

This dataset is showing all pathways identified in indicated group of samples, combined by genotype/group.

Files

• pathDIA_P23H.csv - data generated at UEF, Finland

• pathDIA_Rd10_DR.csv - data generated at UEF, Finland

• pathDDA_RPE65_KO.csv - data generated at UCI, US

• pathDDA_P23H.csv - data generated at UCI, US

• pathDDA_Rd10_DR.csv - data generated at UCI, US

• pathDDA_Rd10_CLR.csv - data generated at UCI, US

  Variables

• ID

  Identifier of the pathway or term (e.g., KEGG ID, GO term ID).

• Description

  Name or description of the pathway or biological term (e.g., "Apoptosis", "Oxidative phosphorylation").

• ProteinRatio

  Proportion of differentially expressed proteins (DEPs) from your dataset found in the pathway:

• BgRatio

  Background ratio — proportion of proteins associated with the pathway in the background (e.g., whole proteome):

• pvalue

  Raw p-value from statistical test (e.g., hypergeometric test) indicating enrichment significance.

• p.adjust

  Adjusted p-value (e.g., using Benjamini-Hochberg correction) to control for multiple comparisons.

• qvalue

  False discovery rate (FDR) estimate — similar to p.adjust, used to assess significance while accounting for multiple testing.

• geneID of included DEPs

  List of gene symbols or IDs for the differentially expressed proteins included in the pathway.

• Count

  Number of DEPs from your dataset found in the pathway.

  This dataset describes characteristics of each group of samples, combined by genotype/group.

  Files

• UCI_DDA_Rpe65-KO_cohort_1.csv - animals at UCI, USA

• UEF_DIA_P23H_cohort_2.csv - animals at UEF, Finland

• UCI_DDA_P23H_cohort_1.csv - animals at UCI, USA

• UEF_DIA_rd10_DR_cohort_3.csv - animals at UEF, Finland

• UCI_DDA_rd10_DR_cohort_2.csv - animals at UCI, USA

• UCI_DDA_rd10_CLR_cohort_1.csv - animals at UCI, USA

  Variables

• Mouse ID

  Unique identifier assigned to each individual mouse.

• File name

  Name of the associated data file (e.g., raw data, image, or analysis file) for that mouse.

• Genotype

  Genetic makeup of the mouse (e.g., WT for wild-type, or a specific mutation like P23H).

• Sex

  Biological sex of the mouse (Male or Female).

• DOB

  Date of Birth — the day the mouse was born.

• Euthanasia date

  The date the mouse was euthanized (sacrificed for analysis).

• Euthanasia Method

  The procedure used for euthanasia (e.g., CO₂ inhalation, cervical dislocation).

• Euthanasia age (days)

  Age of the mouse at the time of euthanasia, calculated in days.

• Housing light condition

  Description of the lighting environment in which the mouse was housed (e.g., 12:12 light-dark cycle, constant darkness).

Access information

All files generated during the proteomic analysis