plotPrefFragPat

plot preferential fragmenation pattern 
Plot preferential fragmenation pattern equivalent to Fig 1b of Haverland et al 2017 (J Am Soc Mass Spectrom)

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

plotPrefFragPat function

<dl><dt>prefPat</dt>
<dd>(matix)</dd>
<dt>namesCex</dt>
<dd>(numeric) expansion factor cex for display of AA-names</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

plot preferential fragmenation pattern
  
Plot preferential fragmenation pattern equivalent to Fig 1b of Haverland et al 2017 (J Am Soc Mass Spectrom) — plotPrefFragPat

<dl>

<dt>prefPat</dt>
<dd>(matix)</dd>


<dt>namesCex</dt>
<dd>(numeric) expansion factor cex for display of AA-names</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>

plotPrefFragPat: plot preferential fragmenation pattern Plot preferential fragmenation pattern equivalent to Fig 1b of Haverland et al 2017 (J Am Soc Mass Spectrom)

Description

Usage

Value

Arguments

See Also

Examples