Peek a peak: a glance at statistics for quantitative label-free proteomics

Abstract

Today, label-free mass spectrometry methods are frequently used for quantification of proteins and peptides. There have been several proposals of measurable parameters that best reflect quantities, such as peak areas as well as spectral counts. This review provides a systematic overview of the proposed methods. Owing to the shotgun proteomics approach generally used today for label-free mass spectrometry, any quantitative measure in the first place is a measure of peptide quantity. There has been no systematic research on how to best infer protein quantity from its measured peptides’ quantities. The way peptide identifications are assembled to protein lists may especially lead to significantly different results in protein quantification. A further focus of this review will thus be the assembly of measured peptide quantities to a protein quantity.

Keywords::

• identification
• label-free
• mass spectrometry
• quantification
• spectral counting

Financial & competing interests disclosure

Proteomics Data Collection (ProDaC) was funded as a Coordination Action by the European Commission (6th framework programme, project number LSHG-CT-2006–036814). National Genome Research Network (NGFN) plus is funded by the Bundesministerium für Bildung und Forschung (BMBF), grant 01 GS 08143. This work is further funded by Cluster Industrielle Biotechnologie (CLIB ) – contract number 616 40003 0315413B. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.