Adv Exp Med Biol
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Since mass spectrometry was introduced as the core technology for large-scale analysis of the proteome, the speed of data acquisition, dynamic ranges of measurements, and data quality are continuously improving. These improvements are triggered by regular launches of new methodologies and instruments.
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Fecal microbiota transplantation (FMT) is a rather straightforward therapy that manipulates the human gastrointestinal (GI) microbiota, by which a healthy donor microbiota is transferred into an existing but disturbed microbial ecosystem. This is a natural process that occurs already at birth; infants are rapidly colonized by a specific microbial community, the composition of which strongly depends on the mode of delivery and which therefore most likely originates from the mother (Palmer et al. 2007; Tannock et al. 1990). Since this early life microbial community already contains most, if not all, of the predominantly anaerobic microbes that are only found in the GI tract, it is reasonable to assume that early life colonization is the ultimate natural fecal transplantation.
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Review
Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.
Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.
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Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. ⋯ With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.
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Endobronchial ultrasound guided transbronchial needle aspiration (EBUS-TBNA) had an enormous impact on the current advancement in diagnostic bronchoscopy. The aims of the present study were: (1) to evaluate the added value of EBUS-TBNA to routine diagnostic bronchoscopy performed in patients with mediastinal lymph node enlargement and (2) to identify factors that affect the diagnostic yield of EBUS-TBNA. We retrospectively analyzed 712 EBUS-TBNA procedures out of the 4081 bronchoscopies performed in the years 2009-2014. ⋯ We conclude that EBUS-TBNA is a valuable diagnostic method in an unselected group of patients with mediastinal lymph node enlargement. The percentage of positive EBUS-TBNA diagnoses is related to lymph node dimensions. The overall efficacy of EBUS-TBNA improves with increasing years of experience.