HPPInspector

Results Views

The HPPInspector workflow has two main results views: 1. The Proteins table, where all input proteins and FDR-controlled evidence supporting them goes 2. The Precursors table, where all precursor variants from input search jobs

Proteins Table

• Protein The full protein string from the input database.
• Protein Accession The Uniprot protein accession, if the FASTA file has one, otherwise the same as the Protein column.
• FDR (See SI for more details)
  • Score (HPP 2+) The protein score for HPP-FDR
  • FDR (HPP 2+) HPP-FDR value
  • Score (Leftover) The protein score for leftover FDR
  • FDR (Leftover) leftover FDR value
  • Score (Canonical Picked) The protein score for canonical picked protein FDR
  • FDR (Canonical Picked) Canonical picked protein FDR value
  • Score (Canonical Traditional) The protein score for canonical protein FDR
  • FDR (Canonical Traditional) Canonical protein FDR value
• Protein Information
  • Protein Type Cateogorization of the Protein Type, either Canonical, Isoform, TrEMBL, or Contaminant
  • View Peptides Link to view all HPP-compliant peptides for the protein
  • Gene Gene name from UniProt (if present in the FASTA file)
  • PE Protein Existence number from the latest release of neXtProt.
  • Protein Length Length of the protein in number of amino acid
• Unique Protein Coverage
  • Total Coverage Percent of amino acids on the protein covered by a peptide mapping to the protein
  • #Sequences Number of unique sequences covering the protein
• HPP Protein Coverage
  • #HPP Peptides (Canonical-unique) Number of non-nested HPP peptides covering the protein in the current job, unique to the gene product
  • #HPP Peptides (Isoform-unique) Number of non-nested HPP peptides covering the protein in the current job, unique to the isoform
  • Coverage Amino acids covering the protein, only in the current job
  • Previously-known Peptides List of all peptides in the current job, that were already in the comparison job
  • Novel Peptides List of all peptides in the current job, that are not in the comparison job
  • #HPP Peptides (Combined) Number of non-nested HPP peptides covering the protein combined between the current job and the previous job
  • #HPP Peptides (Combined, Pass FDR) Number of non-nested HPP peptides from both the current job, both passing HPP FDR
  • #HPP Peptides (Reference Leftover FDR) Number of non-nested HPP peptides from the current job and the comparison job, only passing leftover FDR, not HPP FDR
  • #HPP Peptides (Reference HPP FDR) Number of non-nested HPP peptides passing HPP-FDR in the reference
  • #HPP Peptides (Added Only) Number of non-nested HPP peptides just in the added set
  • Coverage (Total) Amino acids covering the protein, combined between the current job and the comparison job
  • Coverage Increase (All) Percent added coverage between the current job and the comparison job
• HPP Protein Coverage (Synthetic) Only HPP sequences that have matching synthetic sequences are considered. Columns mirror the previous section.
  • Previously-known Peptides (Synthetic)
  • Novel Peptides (Synthetic)
  • #HPP Peptides (Combined) (Synthetic)
  • #HPP Peptides (Reference Leftover FDR) (Synthetic)
  • #HPP Peptides (Reference HPP FDR)(Synthetic)
  • #HPP Peptides (Added Only) (Synthetic)
  • Coverage (Total) (Synthetic)
  • Coverage Increase (Synthetic)
• HPP Protein Coverage (Synthetic + Pass Cosine Threshold) Only HPP sequences that have matching synthetic sequences and have a annotated cosine passing the input threshold are considered. Columns mirror the previous section.
  • Previously-known Peptides (Synthetic + Pass Cosine Threshold)
  • Novel Peptides (Synthetic + Pass Cosine Threshold)
  • #HPP Peptides (Combined) (Synthetic + Pass Cosine Threshold)
  • #HPP Peptides (Reference Leftover FDR) (Synthetic + Pass Cosine Threshold)
  • #HPP Peptides (Reference HPP FDR) (Synthetic + Pass Cosine Threshold)
  • #HPP Peptides (Added Only) (Synthetic + Pass Cosine Threshold)
  • Coverage (Total) (Synthetic + Pass Cosine Threshold)
  • Coverage (Added) (Synthetic + Pass Cosine Threshold)