checkModTy

Check &amp; complete settings for mixed of variable and fixed modifications.
The final format is a list with $basMod, $varMod and $varMo2

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

checkModTy function

<dl><dt>modTy</dt>
<dd>(character) list of modification types to be considered</dd>
<dt>knownMods</dt>
<dd>(character) optonal custom list of known modifications, default from <code>AAfragSettings(outTy="all")$knownMods</code></dd>
<dt>silent</dt>
<dd>(logical) suppress messages</dd>
<dt>debug</dt>
<dd>(logical) additional messages for debugging</dd>
<dt>callFrom</dt>
<dd>(character) allows easier tracking of messages produced</dd></dl>

Arguments

Check &amp; complete mixed of variable and fixed modifications — checkModTy

<dl>

<dt>modTy</dt>
<dd>(character) list of modification types to be considered</dd>


<dt>knownMods</dt>
<dd>(character) optonal custom list of known modifications, default from <code>AAfragSettings(outTy="all")$knownMods</code></dd>


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


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


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

</dl>

checkModTy: Check & complete mixed of variable and fixed modifications

Description

Usage

Value

Arguments

See Also

Examples