.countLET

Count how many time a given letter occurs in each element of 'seq'

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

.countLET function

<dl><dt>sequ</dt>
<dd>(character) eg peptide sequence(s)</dd>
<dt>countCh</dt>
<dd>(charcter)</dd>
<dt>silent</dt>
<dd>(logical) suppress messages</dd>
<dt>debug</dt>
<dd>(logical) for bug-tracking: more/enhanced messages and intermediate objects written in global name-space</dd>
<dt>callFrom</dt>
<dd>(character) allow easier tracking of message(s) produced</dd></dl>

Arguments

Count Letters — .countLET

<dl>

<dt>sequ</dt>
<dd>(character) eg peptide sequence(s)</dd>


<dt>countCh</dt>
<dd>(charcter)</dd>


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


<dt>debug</dt>
<dd>(logical) for bug-tracking: more/enhanced messages and intermediate objects written in global name-space</dd>


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

</dl>

.countLET: Count Letters

Description

Usage

Value

Arguments

See Also

Examples