NAME

MS::Reader::MzML::Spectrum - An MzML spectrum object

SYNOPSIS

    use MS::Reader::MzML;
    use MS::CV qw/:MS/;

    my $run = MS::Reader::MzML->new('run.mzML');

    while (my $spectrum = $run->next_spectrum) {
        
        # $spectrum inherits from MS::Spectrum, so you can do:
        my $id  = $spectrum->id;
        my $rt  = $spectrum->rt;
        my $mz  = $spectrum->mz;
        my $int = $spectrum->int;
        my $lvl = $spectrum->ms_level;

        # $spectrum inherits from MS::Reader::MzML::Record, so you can do:
        my $tc  = $spectrum->param(MS_TOTAL_ION_CURRENT);
        my $sn  = $spectrum->get_array(MS_CHARGE_ARRAY); # if present

        # in addition,

        my $precursor = $spectrum->precursor;
        my $pre_mz    = $precursor->{mono_mz};
        my $pre_mz    = $precursor->{mono_mz};

        my $scan_num  = $spectrum->scan_number;
        my $scan_win  = $spectrum->scan_window;

        # or access the guts directly (yes, it's okay!)
        my $peak_count = $spectrum->{defaultArrayLength};

        # print the underlying data structure
        $spectrum->dump;

    }

DESCRIPTION

MS::Reader::MzML::Spectrum objects represent spectra parsed from an mzML file. The class is an implementation of MS::Spectrum and so implements the standard data accessors associated with that class, as well as a few extra, as documented below. The underlying hash is a nested data structure containing all information present in the original mzML record. This information can be accessed directly (see below for details of the data structure) when class methods do not exist for doing so.

METHODS

id

    my $id = $spectrum->id;

Returns the native ID of the spectrum

mz

    my $mz = $spectrum->mz;
    for (@$mz) { # do something }

Returns an array reference to the m/z data array

int

    my $int = $spectrum->int;
    for (@$int) { # do something }

Returns an array reference to the peak intensity data array

rt

    my $rt = $spectrum->rt;

Returns the retention time of the spectra, in SECONDS

ms_level

    my $l = $spectrum->ms_level;

Returns the MS level of the spectrum as a positive integer

param, get_array

See MS::Reader::MzML::Record

precursor

    my $pre = $spectrum->precursor;
    my $pre_mz = $pre->{mono_mz};

Returns a hash reference containing information about the precursor ion for MSn spectra. Throws an exception if called on an MS1 spectrum. Note that this information is pulled directly from the MSn record. The actual spectrum object for the precursor ion could be fetched e.g. by:

    my $pre_idx = $run->get_index_by_id( 'spectrum' => $pre->{scan_id} );
    my $pre_obj = $run->fetch_spectrum( $pre_idx );

scan_number

    my $scan = $spectrum->scan_number;

Attempts to parse and return the scan number of the spectrum from the spectrum id. Returns the scan number as an integer or undef if it cannot be determined.

NOTE: Currently this is only implemented for Thermo native IDs in the form of "controllerType=0 controllerNumber=1 scan=10001". Hopefully this will be expanded in the future.

scan_window

    my $limits = $spectrum->scan_window;
    my ($lower, $upper) = @$limits;

Returns an array reference to the lower and upper limits of the scan window(s) of the array, in m/z.

CAVEATS AND BUGS

The API is in alpha stage and is not guaranteed to be stable.

Please reports bugs or feature requests through the issue tracker at https://github.com/jvolkening/p5-MS/issues.

SEE ALSO

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

Copyright 2015-2016 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.