Existence of ribosomal protein mass fingerprint of different bacterial, archaeal and eukaryotic species

Ribosomes are known to be highly conserved due to the importance of protein synthesis to cellular maintenance. Thus, constituent ribosomal proteins should theoretically be highly conserved, which implied a conserved amino acid sequence and molecular mass. However, unique molecular mass fingerprint of ribosomal proteins of individual species in the three domains of life was detected. … More Existence of ribosomal protein mass fingerprint of different bacterial, archaeal and eukaryotic species

General structure of the ribosome may be conserved, but small alterations in structural features likely exist between ribosomes of different species

Ribosome are highly conserved in structure and function given their importance to protein synthesis. Comprising a small and large subunit, ribosomes are built up of ribosomal proteins and RNA that provide both structure and function to the macromolecular complex.   Ribosomal proteins, in particular, differ in mass between different species and thus constitute a unique … More General structure of the ribosome may be conserved, but small alterations in structural features likely exist between ribosomes of different species

Conserved mass peaks in mass spectra of bacterial species

Conserved mass peaks were found in mass spectra of individual bacterial species that highlighted a deep biological basis in the use of mass spectrometry for identifying bacteria. Specifically, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could profile biomolecules (mostly proteins) from bacterial cells that result in a mass spectrum useful for identification purposes. While … More Conserved mass peaks in mass spectra of bacterial species

Transfer of laser energy from matrix coating helps prevent fragmentation of molecules

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) ionizes molecules without inducing fragmentation, thereby allowing molecular ion to be detected, which helps data interpretation of mass spectrum. The mechanisms underlying the ability of the mass spectrometry technique to ionize molecules without inducing fragmentation lies in the use of special matrix compounds that help transfer laser … More Transfer of laser energy from matrix coating helps prevent fragmentation of molecules

Genomics enabled mass spectrometry-based proteomics

Mass spectrometry has developed into a critical tool for proteomics where a large number of studies had used mass spectrometry instruments for profiling the proteome of cells and tissues. However, identification of the mass peaks profiled in the mass spectrum would require the support of a library of molecular mass of all proteins profiled in … More Genomics enabled mass spectrometry-based proteomics

Inability to constrain metabolic models with growth data in the absence of compositional changes in medium

The goal of metabolic modelling is to determine the metabolic flux through specific pathways in the cell. Doing so requires data on cell growth (whether microbes or human cells) as well as compositional data of the growth medium given that cellular metabolic activities would consume nutrients as well as generate byproducts that accumulate in the … More Inability to constrain metabolic models with growth data in the absence of compositional changes in medium

Protein identification is the key challenge in proteomics

Proteomics seek to uncover the ensemble of proteins within a cell or the cell surface. However, whether assisted by mass spectrometry or Western Blot, the key challenge in proteomics remain the identification of proteins. Protein identification remains laborious and time expensive even in the case of mass spectrometry-based proteomics where the challenge lies in the … More Protein identification is the key challenge in proteomics

Challenges of protein identification by MALDI-TOF mass spectrometry

The gold standard approach for identifying a protein is Western blot, which uses a primary antibody to recognize the target protein for subsequent visualization of the protein band by chemiluminescence. More recently, various mass spectrometry-based methods have been developed for the detection and identification of proteins.   These techniques could be classified into fragmentation-based methods … More Challenges of protein identification by MALDI-TOF mass spectrometry

Role of organic particles in seeding growth of aerosols in the atmosphere

Article in Nature, Vol. 533, 26 May 2016, pp. 527, “The role of low-volatility organic compounds in initial particle growth in the atmosphere”   Summary of article: Using nitrate ion chemical ionization atmospheric pressure interface time of flight mass spectrometry, a particle growth model for organic aerosols was proposed and validated.   Comment: Organic materials … More Role of organic particles in seeding growth of aerosols in the atmosphere

Understanding past climate from bubbles trapped in ice cores

We know the past from a historical record of it written on paper, inscribed in stone, or from depictions of events entrapped in fossils. To understand past climates, scientists look for bubbles of past atmospheres trapped in ice cores as historical record of what happened. Typically, these ice cores could be obtained from three types … More Understanding past climate from bubbles trapped in ice cores