spikeins

A subset of the Bruderer 2015 dataset containing 12 spike-in proteins. The full dataset was exported from the Spectronaut software. The complete dataset has been median-normalized.

datasets

An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.

Thang Pham

Protein Quantification in Mass Spectrometry-Based Proteomics

Alex Henneman

spikeins function

A data frame with 18189 observations on the following 9 variables.<dl>
 <dt><code>R.Condition</code></dt>
<dd>Sample names.</dd> <dt><code>PG.ProteinGroups</code></dt>
<dd>Protein identifiers.</dd> <dt><code>EG.ModifiedSequence</code></dt>
<dd>Sequence of the fragment ions.</dd> <dt><code>FG.Charge</code></dt>
<dd>Fragment group charge.</dd> <dt><code>F.FrgIon</code></dt>
<dd>Fragment ions.</dd> <dt><code>F.Charge</code></dt>
<dd>Fragment charges.</dd> <dt><code>F.PeakArea</code></dt>
<dd>Quantitative values.</dd> <dt><code>PG.Genes</code></dt>
<dd>Gene names.</dd> <dt><code>PG.ProteinNames</code></dt>
<dd>Protein names.</dd> 
</dl>

Format

An example dataset of 12 spike-in proteins — spikeins

A data frame with 18189 observations on the following 9 variables.<dl>
 <dt><code>R.Condition</code></dt>
<dd>Sample names.</dd>

 <dt><code>PG.ProteinGroups</code></dt>
<dd>Protein identifiers.</dd>

 <dt><code>EG.ModifiedSequence</code></dt>
<dd>Sequence of the fragment ions.</dd>

 <dt><code>FG.Charge</code></dt>
<dd>Fragment group charge.</dd>

 <dt><code>F.FrgIon</code></dt>
<dd>Fragment ions.</dd>

 <dt><code>F.Charge</code></dt>
<dd>Fragment charges.</dd>

 <dt><code>F.PeakArea</code></dt>
<dd>Quantitative values.</dd>

 <dt><code>PG.Genes</code></dt>
<dd>Gene names.</dd>

 <dt><code>PG.ProteinNames</code></dt>
<dd>Protein names.</dd>

 
</dl>

spikeins: An example dataset of 12 spike-in proteins

Description

Usage

Arguments

Format

Examples