This function calculates the (monoisotopic) mass over charge ratio (m/z) for peptides, as measured in mass spectrometry.

Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.

Daniel Osorio

Peptides

Calculate Indices and Theoretical Physicochemical Properties of
Protein Sequences

Paola Rondon-Villarreal

Rodrigo Torres

J. Sebastian Paez

Luis Pedro Coelho

Richèl J.C. Bilderbeek

Florian C. Sigloch

mz function

<dl><dt>seq</dt>
<dd>An amino-acids sequence, in one letter code.</dd>
<dt>charge</dt>
<dd>The net charge for which the m/z should be calculated</dd>
<dt>label</dt>
<dd>Set a predefined heavy isotope label. Accepts "none", "silac_13c", "silac_13c15n" and "15n". Overwrites input in <code>aaShift</code>.</dd>
<dt>aaShift</dt>
<dd>Define the mass difference in Dalton of given amino acids as a named vector. Use the amino acid one letter code as names and the mass shift in Dalton as values.</dd>
<dt>cysteins</dt>
<dd>Define the mass shift in Dalton of blocked cysteins. Defaults to 57.021464, for cysteins blocked by iodoacetamide.</dd></dl>

Arguments

Calculate the m/z for peptides. — mz

<dl>

<dt>seq</dt>
<dd>An amino-acids sequence, in one letter code.</dd>


<dt>charge</dt>
<dd>The net charge for which the m/z should be calculated</dd>


<dt>label</dt>
<dd>Set a predefined heavy isotope label. Accepts "none", "silac_13c", "silac_13c15n" and "15n". Overwrites input in <code>aaShift</code>.</dd>


<dt>aaShift</dt>
<dd>Define the mass difference in Dalton of given amino acids as a named vector. Use the amino acid one letter code as names and the mass shift in Dalton as values.</dd>


<dt>cysteins</dt>
<dd>Define the mass shift in Dalton of blocked cysteins. Defaults to 57.021464, for cysteins blocked by iodoacetamide.</dd>

</dl>

mz: Calculate the m/z for peptides.

Description

Usage

Arguments

Examples