Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

Abstract

With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization of posttranslational modifications. It is furthermore common practice to quantify the identified entities, a task supported by a panel of different methods. Finally, the results can also be enriched with functional knowledge gained on the proteins, detecting for instance differentially expressed gene ontology terms or biological pathways.In this study, we review the resources, methods and tools available for the researcher to achieve such a quantitative functional analysis. These include statistics for the postprocessing of identification and quantification results, online resources and public repositories. With a focus on free but user-friendly software, preferably also open-source, we provide a list of tools designed to help the researcher manage the vast amount of data generated. We also indicate where such applications currently remain lacking. Moreover, we stress the eventual pitfalls of every step of such studies.

Quantitative Proteomics Analysis of Altered Protein Expression in the Placental Villous Tissue of Early Pregnancy Loss Using Isobaric Tandem Mass Tags

“…Recently, proteomics technologies have become sufficiently advanced enough that it is now realistic to measure clinical material to investigate pregnancy-related illnesses such as preeclampsia, Down syndrome pregnancies, and other such conditions [11–14]. The comparison of the proteome of interest between the healthy and disease state thus provides a fine-grained picture of the regulations involved [15]. In 2006, Liu et al extracted protein from the placental villous tissue of two groups (six placental villous tissues with early pregnancy loss and six from normal pregnant women).…”

New Technologies for Studying Biofilms

“…Two rapidly expanding approaches within this field are proteomics and metabolomics (180, 181). From an information standpoint, proteomics and metabolomics are a step closer to biofilm physiology than genomics and transcriptomics, since the proteins and metabolites are biomolecules that comprise most of the enzymatic activity of the cells and the metabolic substrates and products of those enzymes.…”

“…From an information standpoint, proteomics and metabolomics are a step closer to biofilm physiology than genomics and transcriptomics, since the proteins and metabolites are biomolecules that comprise most of the enzymatic activity of the cells and the metabolic substrates and products of those enzymes. However, neither proteomics nor metabolomics provide data sets that are as complete as methods focused on nucleic acids (180, 181). It is now routine to obtain deep coverage of transcribed regions of a genome using transcriptomics approaches, but there has yet to be a truly comprehensive proteomics or metabolomics investigation.…”

The application of proteomic technologies for the analysis of muscle proteins of farm animals used in the meat industry (Review)

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