CycloBranch
Sequence/Compound Database Editor

Sequence/Compound Database Editor

The editor is opened using the command "Tools -> Sequence/Compound Database Editor" from the Main Window. Use F1 to open this help.

Changes in the editor do not impact the settings of the engine until they are saved !

sequenceeditor.png
Sequence/Compound Database Editor

Toolbar

New Database (CTRL + N)

Create a new database of sequences/compounds.

Open Database (CTRL + O)

Open a database of sequences/compounds.

Save Database (CTRL + S)

Save the database of sequences/compounds.

Save Database As... (CTRL + D)

Save the database of sequences/compounds with another file name.

Import Database (CTRL + I)

Import a database of sequences/compounds.

Close (Esc)

Close window.

Insert Row (Insert)

Insert a new row at the bottom of the table.

Remove Selected Rows (Delete)

Remove checked rows.

Select All (CTRL + A)

Select all rows.

Unselect Rows (CTRL + U)

Unselect all rows.

HTML Documentation (F1)

Show HTML documentation.

Text Filter

See details here.

Columns

  • Type - The type of a peptide (linear, cyclic, branched, branch-cyclic, linear-polyketide or cyclic-polyketide).
  • Name - Name of a peptide.
  • Summary Formula - Summary formula of a neutral molecule.
  • Monoisotopic Mass - Monoisotopic mass of the peptide. The value is recalculated when the summary formula is changed.
  • Sequence - Peptide sequence. If the column is empty, the database can be utilized for identification of compounds in MS spectra. If the column is non-empty, the database can be used in both MS and MS/MS mode.
  • N-terminal Modification - A name of an N-terminal modification of a linear or a branched peptide.
  • C-terminal Modification - A name of a C-terminal modification of a linear or a branched peptide.
  • Branch Modification - A name of an N-terminal or a C-terminal modification of a branch of a branched or a branch-cyclic peptide.
  • Reference - Reference id of a peptide. See Format of Sequence Databases.
  • View - View the molecule structure in a reference database (ChemSpider, PubChem or Norine).

Format of Sequence Databases

The database of sequences is a text file (*.txt) containing a list of sequences (one sequence per line). Each line contains the following items separated by tabulars:

  • type of a sequence (linear, cyclic, branched, branch-cyclic, linear-polyketide or cyclic-polyketide)
  • name of a peptide
  • summary formula of a neutral molecule
  • monoisotopic mass of peptide (the value is ignored; the mass is automatically calculated from the summary formula)
  • a peptide sequence
  • name of an N-terminal modification
  • name of a C-terminal modification
  • name of a branch modification
  • reference id of a peptide

A line starting with the hash '#' is a comment which is not processed.

The format of a peptide sequence differs according to a peptide type:

  • Linear peptide: [aaa/bbb]-[ccc]-[ddd]-[eee]-[fff]. The names of building blocks must be enclosed in [ and ]. The building blocks are separated by -. Isomers of a building block are separated by /.
  • Cyclic peptide: the same syntax like in case of a linear peptide.
  • Branched peptide: [aaa/bbb]\([ccc]-[ddd]-[eee]\)[fff]. The syntax is similar to a linear peptide. The string \( is used instead of - to determine the start of a branch. The string \) is used instead of - to determine the end of a branch. The building block [ccc] is the block where the branching occurs. The building block [eee] is the terminal block of the branch. See also Branched Peptides.
  • Branch-cyclic peptide: the same syntax like in case of a branched peptide.
  • Linear polyketide: the same like in case of a linear peptide (acronyms of building blocks eliminating 2 hydrogens can be included in the sequence).
  • Cyclic polyketide: the same like in case of a cyclic peptide (acronyms of building blocks eliminating 2 hydrogens can be included in the sequence).

Reference ids can be written in the following formats (without quotes):

  • "CSID: <number>" (ChemSpider ID; example: "CSID: 13539649")
  • "CID: <number>" (PubChem ID; example: "CID: 12439044")
  • "<norine_id>" (Norine ID; example: "NOR00205")
  • "<lipidmaps_id>" (LipidMaps ID; example: "LMFA00000001")

List of Available Sequence/Compound Databases

All sequence databases can be also used as databases of compounds in MS/MSI mode. See Dereplication. The following databases of are available in "SequenceDatabases" folder:

LocationContentMode
inhouse.txt12 linear, cyclic, branched and branch-cyclic NRP sequences from an in-house collectionMS, MSI, MS/MS
norine-07-2013-linear.txt310 linear NRP sequences exported from Norine (version July, 2013)MS, MSI, MS/MS
norine-07-2013-cyclic.txt443 cyclic NRP sequences exported from Norine (version July, 2013)MS, MSI, MS/MS
norine-07-2013-branched.txt5 branched NRP sequences exported from Norine (version July, 2013)MS, MSI, MS/MS
norine-07-2013-branch-cyclic.txt283 branch-cyclic NRP sequences exported from Norine (version July, 2013)MS, MSI, MS/MS
norine-07-2013.txt1041 linear, cyclic, branched and branch-cyclic NRP sequences exported from Norine (version July, 2013)MS, MSI, MS/MS
siderophores/inhouse_siderophores.txt18 NRP and polyketide siderophores (compiled in-house)MS, MSI, MS/MS
siderophores/709_siderophores_and_secondary_metabolites.txt709 siderophores and Aspergillus secondary metabolites (compiled in-house)MS, MSI
metabolites/all_metabolites.txt850 metabolites of Alternaria, Aspergillus, Candida albicans, Cladosporium, Eurotium, Fennellia, Metarrhizium, Paecilomyces, Phoma, and Trichothecium genera (compiled in-house)MS, MSI
metabolites/alternaria.txt138 metabolites of Alternaria (compiled in-house)MS, MSI
metabolites/aspergillus.txt306 metabolites of Aspergillus (compiled in-house)MS, MSI
metabolites/candida_albicans.txt11 metabolites of Candida albicans (compiled in-house)MS, MSI
metabolites/cladosporium.txt54 metabolites of Cladosporium (compiled in-house)MS, MSI
metabolites/eurotium_and_fennellia.txt44 metabolites of Eurotium and Fennellia (compiled in-house)MS, MSI
metabolites/metarrhizium.txt79 metabolites of Metarrhizium (compiled in-house)MS, MSI
metabolites/paecilomyces.txt97 metabolites of Paecilomyces (compiled in-house)MS, MSI
metabolites/phoma.txt52 metabolites of Phoma (compiled in-house)MS, MSI
metabolites/trichothecium.txt69 metabolites of Trichothecium (compiled in-house)MS, MSI
lipids/LMSD_*_All.txtAll lipids (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_FA.txtFatty Acyls (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_GL.txtGlycerolipids (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_GP.txtGlycerophospholipids (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_PK.txtPolyketides (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_PR.txtPrenol Lipids (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_SL.txtSaccharolipids (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_SP.txtSphingolipids (compiled from http://www.lipidmaps.org/)MS, MSI
lipids/LMSD_*_ST.txtSterol Lipids (compiled from http://www.lipidmaps.org/)MS, MSI
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