scorePrefFrag

Search for preferential fragmentation sites from 'pepTab' among the 3 colums specified via 'useCol' (for full AA sequence, preceeding AA, tailing AA) 
and return sum of scores (from 3rd column of prefFragPat) for both ends.
Note : proteins must be witten as single lettre code.

Top-Down mass spectrometry aims to identify entire proteins as well as their (post-translational) modifications or ions bound (eg Chen et al (2018) <doi:10.1021/acs.analchem.7b04747>).
The pattern of internal fragments (Haverland et al (2017) <doi:10.1007/s13361-017-1635-x>) may reveal important information about the original structure of the proteins studied
(Skinner et al (2018) <doi:10.1038/nchembio.2515> and Li et al (2018) <doi:10.1038/nchem.2908>).
However, the number of possible internal fragments gets huge with longer proteins and subsequent identification of internal fragments remains challenging,
in particular since the the accuracy of measurements with current mass spectrometers represents a limiting factor.
This package attempts to deal with the complexity of internal fragments and allows identification of terminal and internal fragments from deconvoluted mass-spectrometry data.

Wolfgang Raffelsberger

wrTopDownFrag

Internal Fragment Identification from Top-Down Mass Spectrometry

scorePrefFrag function

<dl><dt>pepTab</dt>
<dd>(matrix) peptide-fragments with lines for peptides, cols as sequence/preceedingAA/tailingAA</dd>
<dt>useCol</dt>
<dd>(character) column names for peptide-sequence,preceeding and tailing AA</dd>
<dt>prefFragPat</dt>
<dd>(matrix) for preferential fragmentation rules (see <code>.prefFragPattern()</code>)</dd>
<dt>silent</dt>
<dd>(logical) suppress messages</dd>
<dt>debug</dt>
<dd>(logical) additional messages and objects exportet to current session for debugging</dd>
<dt>callFrom</dt>
<dd>(character) allow easier tracking of messages produced</dd></dl>

Arguments

Identifcation and scoring of preferential cuting sites — scorePrefFrag

<dl>

<dt>pepTab</dt>
<dd>(matrix) peptide-fragments with lines for peptides, cols as sequence/preceedingAA/tailingAA</dd>


<dt>useCol</dt>
<dd>(character) column names for peptide-sequence,preceeding and tailing AA</dd>


<dt>prefFragPat</dt>
<dd>(matrix) for preferential fragmentation rules (see <code>.prefFragPattern()</code>)</dd>


<dt>silent</dt>
<dd>(logical) suppress messages</dd>


<dt>debug</dt>
<dd>(logical) additional messages and objects exportet to current session for debugging</dd>


<dt>callFrom</dt>
<dd>(character) allow easier tracking of messages produced</dd>

</dl>

scorePrefFrag: Identifcation and scoring of preferential cuting sites

Description

Usage

Value

Arguments

See Also

Examples