Tools for Label-free Peptide Quantification

Sven Nahnsen, Chris Bielow, Knut Reinert, Oliver Kohlbacher
<span title="2012-12-17">2012</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
The increasing scale and complexity of quantitative proteomics studies complicate subsequent analysis of the acquired data. Untargeted label-free quantification, based either on feature intensities or on spectral counting, is a method that scales particularly well with respect to the number of samples. It is thus an excellent alternative to labeling techniques. In order to profit from this scalability, however, data analysis has to cope with large amounts of data, process them automatically,
more &raquo; ... do a thorough statistical analysis in order to achieve reliable results. We review the state of the art with respect to computational tools for label-free quantification in untargeted proteomics. The two fundamental approaches are feature-based quantification, relying on the summed-up mass spectrometric intensity of peptides, and spectral counting, which relies on the number of MS/MS spectra acquired for a certain protein. We review the current algorithmic approaches underlying some widely used software packages and briefly discuss the statistical strategies for analyzing the data. Molecular & Cellular
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1074/mcp.r112.025163</a> <a target="_blank" rel="external noopener" href="">pmid:23250051</a> <a target="_blank" rel="external noopener" href="">pmcid:PMC3591650</a> <a target="_blank" rel="external noopener" href="">fatcat:7otlf6bpnrginfkaihiprxsljq</a> </span>
<a target="_blank" rel="noopener" href="" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href=""> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / </button> </a> <a target="_blank" rel="external noopener" href="" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> </button> </a>