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Table 2 Overview of the individual terms (descriptors) of the protein species nomenclature

From: Finding one's way in proteomics: a protein species nomenclature

Level

Comment

Descriptor

A: Gene

Entry name (gene name + species)

G_ACE_humana

B: Nucleotide polymorphism

SNP Accession number

SNP_rs10853044

C: Initial amino acid sequence of the protein synthesized at the ribosome

Accession number (AC) + sequence version (_1)

AC_ P12821-1_1

 

Splicing variant (S) with deletion _ localisation of the deletion

SD_70-79

 

Splicing variant with insertion _ localisation of the insertion

SI_43_ LLELFVMFL

 

Splicing variant with an exchange of amino acids

SE_38_RQELWQG_SKEHWNQb

D: Proteolysis

Truncated amino acids: 1-17: the first 17 amino acids were removed

T_1-17

E: Posttranslational Modification (P)

Position of the modified amino acid

P_33_21c

F: Cofactor (C)

Identity of non-covalently bound cofactors

C_Zn(2x)d

G: Further descriptors

Can be added, if necessary

X, Y

  1. aaccording to the term in the UniProt knowledgebase [35]
  2. b38 indicates the number of the first exchanged amino acid of the peptide. SKEHWNQ is the peptide present in the protein species, which was substituted for RQELWQG.
  3. c the first number (here: 33) gives the position of the modified amino acid; the second number gives the type of the post-translational modification according to the UniMod [6] accession number (here: 21 indicating a phosphorylation)
  4. d here the term indicates the presence of 2 cations of Zn