Free massspec viewspectrum realvshyppeptide software for linux

MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico.

SYNOPSIS

use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;

my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";

my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);

my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;

MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.

Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.

MassSpec::CUtilities is a Perl extension containing C utilities for use in mass spectrometry.

SYNOPSIS

MassSpec::CUtilities is an XS module so theres a chance that you or your target user might not get it to install cleanly on the target system; therefore its recommended to make its presence optional and to offer slower-performing Perl equivalents where practical.

Also note that this module uses a 19-letter amino alphabet rather than the traditional 20-letter alphabet, since the isobars Leucine(L) and Isoleucine(I) are represented instead by "X." Furthermore some portions of this module assume that their input peptides are internally in alphabetical order.

my $haveCUtilities;
if (eval require MassSpec::CUtilities) {
import MassSpec::CUtilities;
$haveCUtilities = 1;
} else {
$haveCUtilities = 0;
}
if ($haveCUtilities) {
my $candidate = MassSpec::CUtilities::encodeAsBitString("ACCGT");
my @shortPeptides = ("ACT","CCGM","ACCGTY","CCT");
my (@list,@answer);
foreach $_ (@shortPeptides) {
push @list, MassSpec::CUtilities::encodeAsBitString($_);
}
if (MassSpec::CUtilities::testManyBitStrings($candidate,@shortPeptides,@list,@answer)) {
# should print "ACT" and "CCT" only
print "Matched: " . join(,,@answer) . "n";
}
}

see API documentation for other available subroutines

ABSTRACT

An eclectic mix of C utilities originally used in a mass spectrometry denovo sequencing project at NIH. It includes a fast Huffman decoder suitable (with minor modifications) for use with the CPAN module Algorithm::Huffman, as well as a fast peptide mass calculator and methods for encoding peptides as products of prime numbers or as bitmaps.

An eclectic mix of C utilities originally used in a mass spectrometry denovo sequencing project at NIH. It includes a fast Huffman decoder suitable (with minor modifications) for use with the CPAN module Algorithm::Huffman, as well as a fast peptide mass calculator and methods for encoding peptides as products of prime numbers or as bitmaps.