corInDelShift

The protein sequence and composition of most proteomes cannot be well mimicked by pure random sequences.
Thus, random sequences (for comparing the quality of fitting) shhould be corrected accordingly, this vector provides help to do so.
This function loads corMutShift- or corInDelShift-values from RData. 
The vector contains possible mass alterations for random drawing either by mutating a given aminoacid (<code></code>corMutShift),
or by making or in/del changes (<code></code>corInDelShift). These values are based on simulations in the human proteome (from UniProt).

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

corInDelShift function

<dl><dt>fi</dt>
<dd>(character) file (and path) to RData to read as corMutShift or corInDelShift. The file when opend must contain a numeric vector either called 'corMutShift' or 'corInDelShift'.</dd></dl>

Arguments

Corrective Values For Random Sequences For In/Dels — corInDelShift

<dl>

<dt>fi</dt>
<dd>(character) file (and path) to RData to read as corMutShift or corInDelShift. The file when opend must contain a numeric vector either called 'corMutShift' or 'corInDelShift'.</dd>

</dl>

corInDelShift: Corrective Values For Random Sequences For In/Dels

Description

Usage

Value

Arguments

See Also

Examples