Unimod Database Fields

Accession #: Automatically assigned to each new entry.

PSI-MS Name: The standard short name for a modification, agreed by members of the protein modification workgroup of the Proteomics Standards Initiative. This field is display only, and may sometimes be copied from the interim name suggested by the record curator. Must be unique within the database.

Interim Name: Descriptive, one word name, suitable for use in software applications. If you adhere the Naming guidelines, it is possible that the Interim Name will be adopted as the "official" PSI-MS Name.

Don't include the specificity as part of the short name. For example, Carboxymethyl is the short name, not Carboxymethyl-Cys or Carboxymethyl (C).

Must be unique within the database. Required

Description: A full name for the modification. Should be descriptive and authoritative. Must be unique within the database. Required

Alt. Description: Alternative description(s). As many as appropriate.

Composition: The chemical composition of the modification as a delta between the modified and unmodified residue or terminus. For example, if the modification removes an H and adds a CH₃ group, the Composition would be shown as H(2) C. The formula is displayed and entered as 'atoms', optionally followed by a number in parentheses. The number may be negative and, if there is no number, 1 is assumed. Hence, H(2) C is the same as H(2) C(1) Required

The atom terms are separated by spaces, and order is not important. Atoms can be either elements or molecular sub-units. Note that C, F, H, etc. are symbols for elements, not one letter codes for amino acids. See symbols & mass values for the current list of atoms..

Specificity: There must be at least one valid Specificity block, and can be as many as necessary.

Site: Chosen from a controlled list of categories. Choose "N-term" or "C-Term" if the modification applies to a terminus independent of the identity of the terminal residue, (e.g. methylation of a carboxy terminus). Required

Position: Chosen from a controlled list of categories. Choose "Anywhere" if the modification applies to a residue independent of its position, (e.g. oxidation of methionine). Choose "Any N-term" or "Any C-term" if the modification applies to a residue only when it is at a peptide terminus, (e.g. conversion of methionine to homoserine). Choose "Protein N-term" or "Protein C-term" if the modification only applies to the original terminus of the intact protein, not new peptide termini created by digestion, (e.g. post-translational acetylation of the protein amino terminus). If Site was specified as "N-term" or "C-Term", then "Anywhere" becomes equivalent to "Any N-term" or "Any C-term". Required

Classification: Chosen from a controlled list of categories. If you would like additional categories defined, please email details to unimod@unimod.org Required

Neutral Loss: Some modifications exhibit a neutral loss on fragmentation. For example, phosphorylation of S or T usually exhibits a loss of 98 Da (H₃PO₄). If this is the case, then enter the chemical composition of the net loss using the same rules as described under Composition. Otherwise, leave blank. Note that this is a loss from the fragment ions, not from the precursor molecular ion.

Comment: Optional comment relating to a particular specificity, (e.g. 'rare' or 'only at low pH'), rather than notes that apply to the modification record as a whole.

References: Optional, but please try to provide at least one reference for each modification. If a Source is chosen, then there must be text in the Reference field, and vice versa. There can be as many references as appropriate.

Source: Chosen from a controlled list of categories. If you would like additional categories defined, please email details to unimod@unimod.org

Reference Text: Accompanying text. For example, a database cross-reference or literature citation. Where possible, the reference should be formatted as a hyperlink. The requirements to create a hyperlink are:

• PubMed PMID

  Enter the PubMed identifier in the Reference Text field. This must be a simple number, e.g. 15650407. Leave Reference URL empty.

• CAS Registry

  Enter the chemical name followed by the CAS Registry identifier in square brackets in the Reference Text field. For example, dansyl chloride [605-65-2]. Leave Reference URL empty.

• CarbBank

  Enter the CarbBank identifier in the Reference Text field. This must be a simple number, e.g. 48471. Leave Reference URL empty.

• RESID

  Enter the RESID identifier in the Reference Text field, e.g. AA0181. Leave Reference URL empty.

• Swiss-Prot

  Enter the Swiss-Prot ID or AC in the Reference Text field, e.g. INS_HUMAN or P01308. Leave Reference URL empty.

• Prosite

  Enter the Prosite in the Reference Text field, e.g. PDOC00304. Leave Reference URL empty.

• Entrez

  Enter any identifier known to Entrez in the Reference Text field, e.g. CAA42669 or gi|412163 or INS_HUMAN or 15650407. Leave Reference URL empty.

• FindMod

  Enter the FindMod abbreviation in the Reference Text field, e.g. PHOS. Leave Reference URL empty.

• Book, Journal, Misc. URL, Other

  Enter the text to be displayed in the Reference Text field, e.g. SILAC overview. Enter the URL for the hyperlink in the Reference URL field, e.g. http://www.pil.sdu.dk/silac_intro.htm.

Notes: Optional free text notes that apply to the modification record as a whole.

Verified: Set to Yes when a new or edited record has been verified by an administrator. This field is display only for record curators.