org.expasy.mzjava.proteomics.io.ms.spectrum.msp

Class MspAnnotationResolver

java.lang.Object

org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver

All Implemented Interfaces:

AnnotationResolver

public class MspAnnotationResolver
extends Object
implements AnnotationResolver

Parses annotations from Msp files. The documentation for the msp format can be found in "NIST Library of Peptide Ion Fragmentation Spectra: Version June 2006" and is:

Documentation from NIST

Each annotation field begins with one of the following characters: y, b, a, p, I, or ?. The first three denote ion types formed in peptide fragmentation. p denotes the parent ion, I denotes an immonium ion or internal ion and ? indicates that the peak cannot be assigned to a known cleavage type (including common neutral losses). Symbols y, b or a are followed by an integer, representing the cleaved position in the parent peptide, and then, for neutral loss ions, by –n, where n is the neutral loss in Daltons (note – this is actual mass units, water loss is always -18, for example). 13C isotopic peaks are denoted with a following i (x is used in place of possible isotopic peaks that do not have preceding non-isotopic peaks). If the peak assignment is suspect, an asterisk follows. Multiply charged ions are represented by ^c, where c is the charge. A ‘/’ follows, followed by the difference between measured m/z and theoretical (exact) m/z. Internal ions are represents as Int/seq/ where seq is the sequence of the internal ion. In qtof spectra, immonium ions are represented as IXY, where X is the parent amino acid and Y are letters A,B,C.. used to distinguish different immonium products of the amino acid X.

For these assignments, a tolerance of 0.8 m/z was used. In cases where more than one assignment is given peaks are ordered with the following preference: neutral loss from parent (X-n), y, b or a with no neutral loss, y, b or a with -18 or -17 neutral loss, other losses. If a second assignment is possible, a second, comma-separated full assignment is given. For two assignments of the same class described above, the m/z closer to theoretical is preferred. Also, if multiple losses from the parent are possible, only the one closest to theoretical m/z is kept.

For consensus spectra, a space follows the assignment(s), after which is given the number of replicate spectra having that peak and the minimum number of spectra required for that peak to have been reported – these numbers are separated by a ‘/’. A space follows, after which the median deviation of m/z (in 1/100th of an m/z) of the peaks in the original spectra used to create that peak.

Examples

 "? 13/18 0.4"
 "a3/-0.02 20/20 1.9"
 "a3i/0.98 20/20 0.4"
 

Notes

Isotopes

Fragments that are isotopes have an i or x after the residue number. From the documentation it is not clear how to distinguish between the 1st, 2nd, 3rd etc. isotopes. From looking at .msp files it appears that the difference between measured m/z and theoretical m/z is relative to the fragment without a isotope. Therefore b6x/0.98 can be interpreted as the 1st isotope of b6.

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
MspAnnotationResolver()

Method Summary

Methods

Modifier and Type	Method and Description
protected com.google.common.base.Optional<PepFragAnnotation>	parseBackboneAnnotation(String value, Peptide peptide) Parses annotations like
protected com.google.common.base.Optional<PepFragAnnotation>	parseInternalAnnotation(String value)
protected com.google.common.base.Optional<PepFragAnnotation>	parsePrecursorAnnotation(String value, Peptide peptide) Parses annotations like
List<PepLibPeakAnnotation>	resolveAnnotations(String value, Peptide peptide)
protected Mass	resolveComposition(String neutralLossGroup)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MspAnnotationResolver

public MspAnnotationResolver()

Method Detail

resolveAnnotations

public List<PepLibPeakAnnotation> resolveAnnotations(String value,
                                            Peptide peptide)

Specified by:

resolveAnnotations in interface AnnotationResolver

parseInternalAnnotation

protected com.google.common.base.Optional<PepFragAnnotation> parseInternalAnnotation(String value)

Parameters:

value - the string to parse

Returns:

an Optional containing the annotation if the value can be parsec or Optional.absent() if not

parsePrecursorAnnotation

protected com.google.common.base.Optional<PepFragAnnotation> parsePrecursorAnnotation(String value,
                                                                          Peptide peptide)

Parses annotations like

     p/0.13
     p-18/-0.06
 

Parameters:

value - the string to parse

peptide - precursor peptide

Returns:

an Optional containing the annotation if the value can be parsec or Optional.absent() if not

parseBackboneAnnotation

protected com.google.common.base.Optional<PepFragAnnotation> parseBackboneAnnotation(String value,
                                                                         Peptide peptide)

Parses annotations like

     b6-43i^2/1.48
     b3i/0.38
     z33/0.38
 

Parameters:

value - the string to parse

peptide - precursor peptide

Returns:

an Optional containing the annotation if the value can be parsec or Optional.absent() if not

resolveComposition

protected Mass resolveComposition(String neutralLossGroup)