Find Pairs: The Module for Protein Quantification of the PeakQuant Software Suite

Abstract

Accurate quantification of proteins is one of the major tasks in current proteomics research. To address this issue, a wide range of stable isotope labeling techniques have been developed, allowing one to quantitatively study thousands of proteins by means of mass spectrometry. In this article, the FindPairs module of the PeakQuant software suite is detailed. It facilitates the automatic determination of protein abundance ratios based on the automated analysis of stable isotope-coded mass spectrometric data. Furthermore, it implements statistical methods to determine outliers due to biological as well as technical variance of proteome data obtained in replicate experiments. This provides an important means to evaluate the significance in obtained protein expression data.

Quantitative Proteomics Using Isobaric Labeling: A Practical Guide

“…Many commercial or free proteomic programs support the analysis of isobaric labeling data ( Table 2 ). Some programs, such as Proteome Discoverer (PD), Mascot [125] , MaxQuant [126] , PEAKS Q [127] , Census [128] , ProRata [129] , PQPQ [130] , OpenMS [131] , Trans-Proteomic Pipeline [132] , and PeakQuant [133] , are integrated platforms for the analysis of different kinds of MS data. They can also be used for the analysis of isobaric labeling data.…”

Bioinformatics Challenges and Solutions in Proteomics as Quantitative Methods Mature

“…Two new software packages are also presented in this issue: Eisenacher and colleagues describe the FindPairs module of the PeakQuant software, targeted towards approaches using 15 N labeling, which is not well covered in the most popular open source tools (Eisenacher et al, 2012); Qi and colleagues describe an open source post-processing tool for using the commercial package Progenesis LC-MS (designed solely for label-free analysis), as a tool for the analysis of stable isotope labeling data and Top3 pseudo absolute quantitation (Qi et al, 2012).…”