Raw mass spectrometry intensity data for replicate 1.

Sheet 1 (“proteinGroups”) lists all protein groups identified in the experiment. Sheet 2 (“CON, REV filtered”) lists groups after filtering (using reverse decoy database, etc). Sheet 3 (“LFQ”) is a summary using data from sheet 2. Sheet 1: “proteinGroups” and sheet 2: “CON, REV filtered”. Protein IDs: Ensembl or Uniprot Identifiers of a group of proteins with overlapping sequence, i.e. cannot be distinguished from one another with peptides from this experiment. Majority protein IDs: Proteins with at least half the peptide matches of the leading protein in the group. Peptide counts (all): The number of peptides assigned to this protein group. Peptide counts (razor+unique): The number of unique peptides (not shared with other groups) + razor peptides (can be shared with other groups) assigned to each protein in this group. Peptide counts (unique): The number of unique peptides (peptides which only match this group and no other). Fasta headers: The Uniprot fasta headers for the members of this group, containing accession number, name, description and mass. Number of proteins: The number of proteins in this group. Peptides: The total number of peptides assigned to this group. Razor + unique peptides: The number of razor + unique peptides assigned to this group. Unique peptides: The number of unique peptides (only assigned to this group). Peptides CON1 (or CON2… etc): The number of peptides assigned to this group, in the control (untreated). Peptides SAM1 (or SAM2… etc): The number of peptides assigned to this group, in the sample (R18-treated). Razor + unique peptides CON1: The number of razor + unique peptides assigned to this group in the control (untreated). Razor + unique peptides SAM1: The number of razor + unique peptides assigned to this group in the sample (R18-treated). Unique peptides CON1: The number of unique peptides assigned to this group in the control (untreated). Unique peptides SAM1: The number of unique peptides assigned to this group in the sample (R18-treated). Sequence coverage [%]: Percentage of the lead protein sequence covered by peptides. Unique + razor sequence coverage [%]: Percentage of the lead protein sequence covered by unique + razor peptides. Unique sequence coverage [%]: Percentage of the lead protein sequence covered by unique peptides only. Mol. weight [kDa]: Molecular weight of the protein in kDa. Sequence length: Length of the lead protein sequence. Sequence lengths: Lengths of all proteins in the group. Q-value: The ratio of forward to reverse protein hits (a measure of false discovery rate). Score: The score is calculated by MaxQuant using the formula: Sum PEP Score = ∑i−log10(PEPbest peptide,i), where PEP = Posterior Error Probability. Identification type CON1: Whether this protein group was identified in the control (untreated) by MS/MS or by matching between runs (can increase identification chances). Identification type SAM1: Whether this protein group was identified in the sample (R18-treated) by MS/MS or by matching between runs (can increase identification chances). Sequence coverage CON1 [%]: Percentage of the lead protein sequence covered by peptides in the control (untreated). Sequence coverage SAM1 [%]: Percentage of the lead protein sequence covered by peptides in the sample (R18-treated). Intensity: The summed intensities for all peptides assigned to this group. Intensity CON1: The summed intensities for all peptides assigned to this group in the control (untreated). Intensity SAM1: The summed intensities for all peptides assigned to this group in the sample (R18-treated). LFQ intensity CON1: The normalised intensity for all peptides assigned to this group in the control (untreated). LFQ intensity SAM1: The normalised intensity for all peptides assigned to this group in the sample (R18-treated). MS/MS Count CON1: Peptide spectrum matches in the control (untreated). MS/MS Count SAM1: Peptide spectrum matches in the sample (R18-treated). MS/MS Count: Peptide spectrum matches in the experiment. Only identified by site: If “+”, a modification site alone was used to identify this protein. Reverse: If “+”, this group is likely a false discovery, identified using the reverse decoy database. Potential contaminant: If “+”, this group is a likely contaminant. id: A unique ID for this protein group. Peptide IDs: The IDs of the peptides assigned to this group. Peptide is razor: Shows which peptides are shared with other groups. Mod. peptide IDs: ID to look up these peptides in associated modifications file. Evidence IDs: ID to look up these peptides in associated evidence file. MS/MS IDs: ID to look up these peptides in associated MS/MS summary file. Best MS/MS: IDs of the peptides with the best matching MS/MS spectra for this group. Oxidation (M) site IDs: IDs to look up these peptides in the associated Oxidation data file. Oxidation (M) site positions: Positions of oxidation sites in the lead protein of this group. Sheet 3: LFQ. A summary of proteins identified in the experiment, after filtering. Accession No: The Uniprot Accession ID for this protein. Peptides CON1 (CON2, C5, etc): The number of peptides assigned to this protein in the control (untreated). Peptides SAM1 (SAM 2, S5, etc): The number of peptides assigned to this protein in the sample (R18-treated). Mol. weight [kDa]: The molecular weight of the protein. Score: The score calculated by MaxQuant using the formula: Sum PEP Score = ∑i−log10(PEPbest peptide,i), where PEP = Posterior Error Probability. LFQ intensity CON1: The normalised intensity for all peptides assigned to this group in the control (untreated). LFQ intensity SAM1: The normalised intensity for all peptides assigned to this group in the sample (R18-treated). Protein Name: The Uniprot fasta header(s) for this protein group
(XLSX)