NAME
InSilicoSpectro::InSilico::Peptide - A class for digestion products
SYNOPSIS
use InSilicoSpectro::InSilico::Peptide;
DESCRIPTION
This class role is to model peptides obtained by enzymatic digestion (InSilicoSpectro::InSilico::CleavEnzyme) from a protein sequence (InSilicoSpectro::InSilico::AASequence).
ATTRIBUTES
- sequence
- modif
-
The localized modifications for MS/MS computations or a list of modifications with number of occurence for PMF computations. See method getModifType.
- parentProtein
-
A InSilicoSpectro::InSilico::AASequence object containing the protein sequence from which the peptide has been obtained.
- start
-
Start position in the parent protein sequence.
- end
-
End position in the parent protein sequence.
- readingFrame
-
Useful in case the digested protein sequence came from DNA/RNA translation.
- nTerm
-
Boolean, is the peptide an N-terminal peptide.
- cTerm
-
Boolean, is the peptide a C-terminal peptide.
- enzyme
-
The enzyme that yielded the peptide (useful for mass computations because of NTermGain and CTermGain for "exotic" enzymes); must be of class InSilicoSpectro::InSilico::CleavEnzyme.
- aaBefore
-
Amino acid immediately before the peptide (at its N-terminus).
- aaAfter
-
Amino acid immediately after the peptide (at its C-terminus).
- enzymatic
-
Was the peptide cleaved by the enzyme at its both ends (value 'full'), at its N-terminus only (value 'half-N'), at its C-terminus only (value 'half-C'), or not enzymatic (value 'no').
This method is the accessor/modifier for attribute enzymatic.
- nmc
-
Number of missed cleavages.
- addProton
-
Set to 1 if you want to add the mass of one proton to the peptide mass when it is computed (for PMF). Otherwise either set to 0 or do not set.
METHODS
new(%h|$Peptide)
Constructor. %h is a hash of attribute=>value pairs, $Peptide is a InSilicoSpectro::InSilico::Peptide object, from which the attributes are copied.
Accessors and modifiers
parentProtein([$val])
Returns the parent protein object (InSilicoSpectro::InSilico::AASequence). If $val is given, then the parent protein is set to $val.
The end and start positions are left unchanged by this method, hence do not forget to ajust them if needed. The readingFrame is copied from the protein.
sequence([$val])
Returns the peptide sequence as a string. If $val is given then the peptide sequence is set to $val.
enzyme([$val])
Enzyme accessor/modifier.
location($start, $end, readingFrame)
Returns a vector with (start, end, readingFrame). If $start, $end, and readingFrame are given then it sets them.
start([$val])
Start position accessor/modifier.
end([$val])
End position accessor/modifier.
readingFrame([$val])
readingFrame accessor/modifier: sets readingFrame attribute if $val is given, returns the readingFrame attribute.
nTerm([$val])
NTerm position accessor/modifier.
cTerm([$val])
CTerm position accessor/modifier.
addProton([$val])
aaBefore position accessor/modifier.
aaBefore([$val])
NTerm position accessor/modifier.
aaAfter([$val])
aaAfter accessor/modifier.
enzymatic([$val])
Enzymatic status accessor/modifier.
nmc([$val])
Number of missed cleavages accessor/modifier.
modif([$modif])
Modifications accessor/modifier: sets modifications if $modif, a reference to vector of modification names or a string is given (see Pheny::InSilico::MassCalculator::variablePeptide function for instance), returns a reference to a vector of modifications. This vector can be converted into a string for display purpose by the Pheny::InSilico::MassCalculator::modifToString function.
modifAt($pos, [$modif])
Accessor/modifier for modification at position $pos. Sets the modification if $modif, a string, is provided.
$pos = 0 is the N-terminal site, $pos = peptide length +1 is the C-terminal site, and 1 <= $pos <= peptide length correspond to amino acids.
To remove a modification set it to an empty string ''.
This method is for localized modifications in view of MS/MS and forces the modification type to be MS/MS (clears previous PMF modifications if any).
addPmfModif($num, $modifName)
Adds a new pair (number of occurence, modification name) to the pmfModif list. This method is for PMF and it forces the modification type to be PMF (clears previous MS/MS modifications if any).
clearModif
Clears modifications.
getModifType
Returns the modification type ('PMF' or 'MS/MS') or undef if no type is defined, i.e. no modifications are set.
getMass
Returns the peptide mass or undefined in case either the peptide sequence is not set or there are variable modifications.
getMoZ(charge)
getLength
Returns peptide sequence length.
I/O
toString
Returns a string made of the amino acids before and after and the peptide sequence. Example 'K.ATURPLJK.S'.
Overloaded "" operator
Returns the string returned by toString.
Prints a complete peptide description.
EXAMPLES
See t/InSilico/testPeptide.pl and t/InSilico/testCalcDigestOOP.pl.
AUTHORS
Jacques Colinge, Upper Austria University of Applied Science at Hagenberg
Alexandre Masselot, www.genebio.com