AAfragSettings

This function provides basic settings for what types of fragments may accomodate which type of modifications : $knownMods: information about which modifications may be considered, $specAAMod: specifc AA sites (if applicable), $specAAMod: specifc AA sites (if applicable).
For example, here 'p' codes for gain of mass for HPO3 only at S, T and Y residues.
Note: $knownMods$Nterm and $knownMods$Cterm are treated as mutually exclusive

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

AAfragSettings function

<dl><dt>outTy</dt>
<dd>(character) default "all" or any of the list-elements</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

Settings For AA Fragmentation — AAfragSettings

<dl>

<dt>outTy</dt>
<dd>(character) default "all" or any of the list-elements</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>

AAfragSettings: Settings For AA Fragmentation

Description

Usage

Value

Arguments

See Also

Examples