ProPepper™ Manual

v1.1.3 – 2017-07-30

 

Table of Content:

  1. Main menu
  2. Records per page and other display options
  3. Search and filter boxes
  4. Up and down arrows in column headers
  5. Proteins
  6. Peptides
  7. Epitopes
  8. Connections
  9. Save to csv

 

1. Main menu

1.1. Proteins

See detailed description of the Protein main menu under 5. Proteins.

  • 1.1.1. Proteins: Currently available complete Poaceae prolamin sequences from Uniprot and links to reference databases (NCBI and Uniprot). Sequences belonging to the same type manually double checked for annotations and corrected based on multiple sequence alignments and characteristic N- and C-terminal sequences (e.g. entry is assigned as LMW-glutenin but based on sequence characteristics it is a gamma-gliadin). Signal peptides were not removed. See detailed description of the Protein submenu under 5.1. Proteins.
  • 1.1.2. GenBank: This table shows nucleotid information related to the protein entry. See detailed description of the Related nucleotids submenu under "5.2.GenBank".

1.2. Peptides

Specific in silico digested peptide entries obtained from the above described proteins using single or multiple enzymatic cleavage tools. Enzymes were trypsin, chymotrypsin-low specificity, pepsin-pH 1.3, LysC, Thermolysin and Proteinase K. See detailed description of the Peptide main menu under 6. Peptides.

1.3. Epitopes

Epitopes obtained from IEDB database using a filter of Poaceae x Homo sapiens and this database was completed with core celiac specific epitopes reported in literature up to date. See detailed description of the Epitopes main menu under 7. Epitopes.

1.4. Connections

This menu provides direct access to cross searches, which function can be available through Base search, too.

The following connections are available:

 

2. Records per page

Changing the number in the textbox, the number of entries to be displayed can be selected. Various sets of entries can be displayed by selecting one of the display options below the tables, i.e. First, Previous, 1, Next, etc.

 

3. Search and filter boxes

There are more search boxes can be used in ProPepper. The upper search box Filter: above the table is for general search across the full content of the table, while search boxes under column headers are for specific searches only applicable in that column. Results will appear showing all the corresponding data in a row, not only that column.

 

4. Up and down arrows in column headers

Clicking on the arrows in the right hand side of the column header, the entries can be sorted in forward or reverse alphabetical order.

Headers and some entries are equipped with tooltips, hovering the mouse over a header or data entry, the full name, sequence or description will be shown if available.

Identical entries in a column suggest some differences in any of the related column(s). For example, the same sequence is shown in more rows if that sequence belongs to more organisms or genotypes.

 

5. Proteins

5.1. Protein List view

  • 5.1.1. Uniprot ID: The Uniprot accession number of the protein entry can be found in this column with a hyperlink. Clicking on the accession number, the Uniprot website will open showing the data page of that selected entry.
  • 5.1.2. L: Length: Length of the protein entry, number shows the number of aminoacids in the protein sequence.
  • 5.1.3. Protein sequence: Aminoacid sequence of the protein entry is displayed.
  • 5.1.4. Type: Protein entries were aligned and grouped according to N- and C-terminal sequences that are characteristic for a protein group/family (read more under 1.1.1. Proteins).
  • 5.1.5. Organism: The name of organism including subspecieces of the species, from which the protein sequence was identified.
  • 5.1.6. Genotype: The name of genotype, from which the protein sequence was identified.
  • 5.1.7. Gen: Genome: The identifier of the genome to which the protein was annotated.
  • 5.1.8. Chr: Chromosome: The identifier of the Chromosome (ie. 1, 6 or 1A, 6B) where the encoding gene of the protein is located.
  • 5.1.9. Allele: The name of the unique gene variant.
  • 5.1.10. #G: GenBank count: The number of records in GenBank that contains this entry.
  • 5.1.11. GenBank IDs: Identifier of the protein entry as in the GenBank. Entries in this column are equipped with a hyperlink. Clicking on the number, the NCBI website will open showing the GenBank data page of that selected entry. Daily updated via the connection to NCBI. Manually written additional information, where applicable will be updated manually.
  • 5.1.12. View: Clicking on the information sign () in the view column, the full page of that protein entry can be displayed as Protein Record view.

Protein Record view

  • 5.1.12.1. Protein ID: An identification number, which is an ID number of the protein entry and unique in the ProPepper database.
  • 5.1.12.2. Uniprot ID: see 5.1.1.
  • 5.1.12.3. Sequence: see 5.1.3.
  • 5.1.12.4. Sequence length: see 5.1.2.
  • 5.1.12.5. Average Mass: Average mass (M) of the protein
  • 5.1.12.6. Unrecognized aminoacids: the number of aminoacids in the sequence that are marked with X in the sequence (or other letter code that are not included in the basic 20 aminoacids) are listed here. In case of unrecognized aminoacids, the mass of the protein sequence doesn't include that mass of the unrecognized aminoacids.

Table of Related GenBank data

  • 5.1.12.7. GenBank ID: see 5.1.11.
  • 5.1.12.8. Type: see 5.1.4.
  • **5.1.12.9. Species: the name of the species that the host organism of the protein was identified from
  • 5.1.12.10. Organism: see 5.1.5.
  • 5.1.12.11. Genotype: see 5.1.6.
  • 5.1.12.12. PG: Plant genome: Letter codes of genome(s) that the host plant organism has
  • 5.1.12.13. Gen: see 5.1.7.
  • 5.1.12.14. Chr: see 5.1.8.
  • 5.1.12.15. Allele: see 5.1.9.
  • 5.1.12.16. Ref: Reference: literature reference related to the protein genbank details (if available)

Table of Related Digestions

  • 5.1.12.17. Uniprot ID: see 5.1.1.
  • 5.1.12.18. Enzyme: the name of enzyme used for in silico digestion
  • 5.1.12.19. Peptide sequence: peptide sequence obtained from the digestion
  • 5.1.12.20. Pos: start Position in the protein sequence for the obtained peptide sequence
  • 5.1.12.21. Level: level of digestion. When it is 0, the peptide was obtained from a protein, when it is above zero, 1 or more, the peptide was obtained from another peptide that was a result of a previous digestion.
  • 5.1.12.22. Parent enzyme: in case the digestion is a Level 1, parent enzyme is the enzyme or combination of enzymes used in the previous (parent) digestion. Digestion ID can be found in the Protein-Peptide (Digestion) Record view (see 1.4.).
  • 5.1.12.23. Parent Peptide Sequence: Peptide sequence from the parent digestion from which the peptide sequence in 5.1.12.19. was obtained at level 1.
  • 5.1.12.24. P ID: Parent Digestion ID: the unique Propepper identification number of the parent digestion event
  • 5.1.12.25. Aft: Number of Digestions after this Digestion: if available. If it is 1 or above, then one or more subsequent digestions can be related to the peptide entry.
  • 5.1.12.26. View: Clicking on the information signs in the view column, the full page of that protein (blue, ), peptide (red, ) and digestion (orange, ) entry can be displayed as Record view.

Table of Related Protein-Epitope Matching

  • 5.1.12.27. Uniprot ID: see 5.1.1.
  • 5.1.12.28. Prot Type: see 5.1.4.
  • 5.1.12.29. Organism: see 5.1.5.
  • 5.1.12.30. Genotype: see 5.1.6.
  • 5.1.12.31. Gen: see 5.1.7.
  • 5.1.12.32. Chr: see 5.1.8.
  • 5.1.12.33. All: see 5.1.9.
  • 5.1.12.34. Type: Cell type: selectable options for T cell or B cell specific epitopes
  • 5.1.12.35. Core: if the epitope is a core epitope, entry shows Yes, if it is not a core epitope, entry shows No
  • 5.1.12.36. Epi name: name of the epitope as shown in IEDB database
  • 5.1.12.37. Epi Seq: Epitope sequence: peptide sequence of the epitope
  • 5.1.12.38. Disease: name of the disease that is triggered by the epitope sequence
  • 5.1.12.39. Ab: Antibody: antibody that is specific for the epitope
  • 5.1.12.40. MHC: MHC Serotype: data from IEDB
  • 5.1.12.41. Pos: Position: start position in protein sequence for the epitope sequence
  • 5.1.12.42. View: Clicking on the information signs in the view column, the full page of that protein entry (blue, ), epitope entry (red, ) and related proteins-epitopes details (orange, ) can be displayed as Record view.

5.2. GenBank List view

  • 5.2.1. GenBank ID: see 5.1.11.
  • 5.2.2. Type: see 5.1.4.
  • 5.2.3. Species: see 5.1.12.9.
  • 5.2.4. Organism: see 5.1.5.
  • 5.2.5. Genotype: see 5.1.6.
  • 5.2.6. PG: see 5.1.12.12.
  • 5.2.7. Gen: see 5.1.7.
  • 5.2.8. Chr: see 5.1.8.
  • 5.2.9. Allele: see 5.1.9.
  • 5.2.10. #P: Protein count number of records in Uniprot that contain this entry
  • 5.2.11. Uniprot IDs: see 5.1.1., but here is no hyperlink.
  • 5.2.12. Ref: Reference: literature reference related to the protein genbank details
  • 5.2.13. View: Clicking on the information sign () in the view column, the full page of that protein entry can be displayed as Protein Record view.

 

6. Peptides List view

  • 6.1. Peptide Sequence: aminoacid sequence of the peptide
  • 6.2. L: Length: peptide sequence length, number shows the number of aminoacids in the peptide sequence.
  • 6.3. Average Mass: Average mass (M) of the peptide
  • 6.4. [M] Mass: Monoisotopic mass of the peptide
  • 6.5. [M+H]+ Mass: Protonated Monoisotopic mass of the peptide
  • 6.6. #UA: Number of unrecognized aminoacids: in the peptide sequence (see 5.1.12.6.)
  • 6.7. View: View peptide details. Clicking on the information sign () in the view column, the full page of peptide entry can be displayed as Peptide Record view.

Peptide Record view

  • 6.7.1. Peptide ID: An identification number of the peptide, which is unique in the ProPepper database.
  • 6.7.2. Peptide Sequence: see 6.1.
  • 6.7.3. Sequence length: see 6.2.
  • 6.7.4. Average Mass: see 6.3.
  • 6.7.5. Monoisotopic Mass [M]: see 6.4.
  • 6.7.6. Protonated Monoisotopic Mass [M+H]+: see 6.5.
  • 6.7.7. Unrecognized aminoacids: see 5.1.12.6.
  • 6.7.8. Table of Related Digestions: see 5.1.12.17-26.
  • 6.7.9. Table of Related Peptide-Epitope Matching:

Table of Related Peptide-Epitope Matching

  • 6.7.9.1. Peptide sequence: see 6.1.
  • 6.7.9.2. Cell Type: see 5.1.12.34.
  • 6.7.9.3. Core: see 5.1.12.35.
  • 6.7.9.4. Epi Name: see 5.1.12.36.
  • 6.7.9.5. Epi Seq: see 5.1.12.37.
  • 6.7.9.6. Disease: see 5.1.12.38.
  • 6.7.9.7. Ab: see 5.1.12.39.
  • 6.7.9.8. MHC Types: see 5.1.12.40.
  • 6.7.9.9. Pos: see 5.1.12.41.
  • 6.7.9.10. View: View related Peptide details (blue, ), related Epitope details (red, ) and Peptide-Epitope details (orange, ). Clicking on the information sign in the view column, the full page of Record views can be displayed.

 

7. Epitopes List view

  • 7.1. IEDB ID: identification number of the epitope as is in the IEDB database
  • 7.2. Cell Type: see 5.1.12.34.
  • 7.3. Core: see 5.1.12.35.
  • 7.4. Name: name of the epitope see 5.1.12.36.
  • 7.5. Sequence: linear epitope sequence see 5.1.12.37.
  • 7.6. Disease: see 5.1.12.38.
  • 7.7. Antibody: see 5.1.12.39.
  • 7.8. MHC Types: see 5.1.12.40.
  • 7.9. Host: host organism for the epitope
  • 7.10. View: view epitope details as full page Epitope Record view

Epitope Record view

  • 7.10.1. Epitope ID: An identification number, which is unique in the ProPepper database.
  • 7.10.2. IEDB ID: data from IEDB
  • 7.10.3. Core Epitope: see 5.1.12.35.
  • 7.10.4. Name: see 5.1.12.36.
  • 7.10.5. Sequence: see 5.1.12.37.
  • 7.10.6. Table of Related Epitope assays:
  • 7.10.7. Table of Related Proteins-Epitopes Matching, see 5.1.12.27-42.
  • 7.10.8. Table of Related Peptides-Epitopes Matching, see 6.7.9.1-10.

Table of Related Epitope assays

  • 7.10.6.1. IEDB ID: see 7.10.2.
  • 7.10.6.2. Cell Type: see 5.1.12.34.
  • 7.10.6.3. Mod Sequence: Modified Sequence: modified epitope sequence, e.g. FVQQQQQPF ---> FVQQQEQPF.
  • 7.10.6.4. Disease: see 5.1.12.38.
  • 7.10.6.5. Antibody: see 5.1.12.39.
  • 7.10.6.6. MHC Types: see 5.1.12.40.
  • 7.10.6.7. MHC Allele: data from IEDB
  • 7.10.6.8. Host: see 7.9.
  • 7.10.6.9. Ref.: Reference: by clicking on the icon, the link directs to the related publication about the epitope assay

 

8. Connections

** See 1.4. Connections

 

9. Save to csv currently unavailable

  • 9.1. Save to csv: Clicking the Results to CSV, the entire search result can be saved in a csv format, not only the displayed entries but as indicated below the search table: e.g. showing 1 to 50 of 50 entries. At the moment a maximum of 10000 records can be downloaded.