Existing bioinformatics tools for the quantitation of post-translational modifications

Abstract

Mass spectrometry (MS)-based proteomics, by itself, is a vast and complex area encompassing various mass spectrometers, different spectra, and search result representations. When the aim is quantitation performed in different scanning modes at different MS levels, matters become additionally complex. Quantitation of post-translational modifications (PTM) represents the greatest challenge among these endeavors. Many different approaches to quantitation have been described and some of these can be directly applied to the quantitation of PTMs. The amount of data produced via MS, however, makes manual data interpretation impractical. Therefore, specialized software tools meet this challenge. Any software currently able to quantitate differentially labeled samples may theoretically be adapted to quantitate differential PTM expression among samples as well. Due to the heterogeneity of mass spectrometry-based proteomics; this review will focus on quantitation of PTM using liquid chromatography followed by one or more stages of mass spectrometry. Currently available free software, which either allow analysis of PTM or are easily adaptable for this purpose, is briefly reviewed in this paper. Selected studies, especially those related to phosphoproteomics, shall be used to highlight the current ability to quantitate PTMs.

Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins

“…For an overview of the performance of quantification methods in a peptidebased quantification setup, we refer to ref. [40].…”

“…Different experimental methods for peptide quantification and subsequent data analysis to extract abundances from the spectra have been extensively reviewed in refs. [35,40]). For detailed insights into database search and identification of PTMs, see ref.…”

Proteomics of corynebacteria: From biotechnology workhorses to pathogens

“…MS has demonstrated its great potential for the analysis of protein PTMs. Newly developed software and fragmentation technologies, such as ETD, and modification‐specific labeling for relative quantification, such as TMT, have been developed (see 43, 44 for recent reviews). However, only very few studies have undertaken PTM analysis for corynebacteria, and recent MS technologies have not been applied to C. glutamicum and other corynebacteria so far.…”

Amino acid and protein modification by oxygen and nitrogen species

“…In this special issue, the review paper by Dr. Allmer (2010) describes bioinformatic platforms and subsidiary tools for qualitative and quantitative evaluation of proteomics data with PTMs produced by means of current proteomics technology, particularly during high throughput mass spectrometric analyses. A special focus of the review is on non-commercial data analysis tools that can either be used or adapted to quantitate PTMs among samples from LC-MS or LC-MS x measurements.…”