.evalIsoFra

Evaluate selected lines of pepTab of SAME AA-length AND iso-mass for preferential cutting sites.

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

.evalIsoFra function

<dl><dt>x</dt>
<dd>(matrix) main input, must contain cols specified as seqCol and "no","tailAA","precAA"</dd>
<dt>prefFragPat</dt>
<dd>(matrix) specifies preferential fragmentation (which combination of AA to consider cols cTer,nTer,score), default made by <code>.prefFragPattern()</code></dd>
<dt>seqCol</dt>
<dd>(character) column names for the column containing the sequence to search for preferential cutting sites</dd>
<dt>silent</dt>
<dd>(logical) suppress messages</dd>
<dt>debug</dt>
<dd>(logical) additional messages for debugging</dd>
<dt>callFrom</dt>
<dd>(character) allow easier tracking of messages produced</dd></dl>

Arguments

Evaluate Selected Lines Of PepTab — .evalIsoFra

<dl>

<dt>x</dt>
<dd>(matrix) main input, must contain cols specified as seqCol and "no","tailAA","precAA"</dd>


<dt>prefFragPat</dt>
<dd>(matrix) specifies preferential fragmentation (which combination of AA to consider cols cTer,nTer,score), default made by <code>.prefFragPattern()</code></dd>


<dt>seqCol</dt>
<dd>(character) column names for the column containing the sequence to search for preferential cutting sites</dd>


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


<dt>debug</dt>
<dd>(logical) additional messages for debugging</dd>


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

</dl>

.evalIsoFra: Evaluate Selected Lines Of PepTab

Description

Usage

Value

Arguments

See Also

Examples