Alexandre Masselot
and 1 contributors

NAME

IonSeries - Perl class to represent fragment ion series.

SYNOPSIS

use InSilicoSpectro::InSilico::IonSeries

DESCRIPTION

IonSeries class is intended to provide a basic class aimed at representing an entire series of fragment ions. By series we mean all the b++ ions, all the y-2(H2O)-NH3 ions, or all the immonium ions for instance.

ALthough needs may vary (display, further computations, scoring, etc.), we believe that to group fragment ions in series is both convenient (no too many objects created like if we would create one object per fragment) and flexible (one can focus on a specific ion type).

In addition to only represent theoretical masses, IonSeries objects have one attribute to point to an experimental peak in case theoretical masses are metched with an experimental spectrum.

ATTRIBUTES

ionType

The name of the fragment ions in the objects, e.g. b, c, y++, a++-2(NH3), immo.

charge

The charge state.

masses

A reference to a vector that contains all the m/z values of the fragments ion of the series. Masses that are not possibles (loss, too short or too long fragment) are indicated by undef values, i.e. the vector referenced by masses always has the peptide length.

massType

A value that indicates whether the masses are monoisotopic masses (0) or average masses (1).

names

A reference to a vector that contains the names of the fragments. For a terminal ion series it simply the numbers of the fragments 1, 2, ..., n; and for an internal ion series it is a list of the fragment sequences. See masses concerning the vector length and impossible masses.

matchedPeak

A reference to a vector describing an experimental peak (see class InSilicoSpectro::Spectra::ExpSpectrum). This attribute is used in case of match with an experimental spectrum only.

massIndex

The index for getting the mass from the matched peaks.

intensityIndex

The index for getting the intensity from the matched peaks.

METHODS

new([%h|$IonSeries])

Constructor. %h is a hash of attribute=>value pairs, $IonSeries is a InSilicoSpectro::InSilico::IonSeries object, from which the attributes are copied.

ionType([$it])

Accessor/modifier of the attribute ionType.

matches([$it])

Accessor/modifier of the attribute matches.

charge([$z])

Accessor/modifier of the attribute charge.

massIndex([$z])

Accessor/modifier of the attribute massIndex.

intensityIndex([$z])

Accessor/modifier of the attribute intensityIndex.

massType([$mt])

Accessor/modifier of the attribute massType.

masses([$m])

Accessor/modifier of the attribute masses.

names([$n])

Accessor/modifier of the attribute names.

toString

Returns a string containing the list of fragments with their m/z values.

Overloaded "" operator

Returns what is returned by toString.

EXAMPLES

See t/InSilico/testCalcFragOOP.pl.

AUTHORS

Jacques Colinge, Upper Austria University of Applied Science at Hagenberg