MassBank / MassBank2NIST

A converter between MassBank and NIST (and Bruker .library) formats and back
2 stars 2 forks source link

Convert Library "AnnotFormula" to MassBank record #15

Open sneumann opened 10 years ago

sneumann commented 10 years ago
AnnotFormula: 43.0291;  C1H3N2
AnnotFormula: 51.0229;  C4H3
AnnotFormula: 53.0134;  C2H1N2
AnnotFormula: 55.0291;  C2H3N2

into format like http://www.massbank.eu/MassBank/jsp/FwdRecord.jsp?id=EA281801

PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)
  70.0652 C4H8N+ 1 70.0651 1.2
  110.9997 C6H4Cl+ 1 110.9996 0.86
  117.0573 C8H7N+ 1 117.0573 0.08

The AnnotFormula shows "uncharged" fragment formulas, EA has added "+/-" at the end.

schymane commented 10 years ago

MassBank Record Style: Line 1 defines the record format of line 2 or later lines. Examples PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm) PK$ANNOTATION: m/z num {formula unsaturation mass error(ppm)} PK$ANNOTATION: m/z num {type mass error(ppm) formula} PK$ANNOTATION: m/z structure num {type mass error(ppm) formula}

Charge can be auto-implied from ION_MODE. If we don't have the error for AnnotFormula, how about: PK$ANNOTATION: m/z formula If structure present, then e.g. PK$ANNOTATION: m/z formula structure or PK$ANNOTATION: m/z formula putative_smiles 170.0042 C7H7O3S- [CH2]c1ccc(cc1)S(=O)([O-])=O 183.0115 C8H7O3S- O=S([O-])(=O)c1ccc(C=C)cc1 as in http://www.massbank.eu/MassBank/jsp/Dispatcher.jsp?type=disp&id=LIT00035&site=24