.chargeCatchingAA

Return a matrix with charge-catching amino-acids and their assumed strength.
So far, the strength shown/used is set rather empirically.

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

.chargeCatchingAA function

<dl><dt>chargeMode</dt>
<dd>(character) this value may be 'pos' (default) for the positively charged amino-acids K,R and H or, 
if this argument has any other value, than all charged amino-acids (K,R,H, S,T,N,Q, D,E, W and Y) will be considered.</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

Cite Charge Catching Amino-Acids — .chargeCatchingAA

<dl>

<dt>chargeMode</dt>
<dd>(character) this value may be 'pos' (default) for the positively charged amino-acids K,R and H or, 
if this argument has any other value, than all charged amino-acids (K,R,H, S,T,N,Q, D,E, W and Y) will be considered.</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>

.chargeCatchingAA: Cite Charge Catching Amino-Acids

Description

Usage

Value

Arguments

See Also

Examples