Metagenomics for identification of microbes

The culture-independent technique of metagenomics offers a way to understand microbial diversity in the absence of the ability to culture most of the microorganisms in the environment. Specifically, the method uses polymerase chain reaction (PCR) and 16S rRNA gene sequencing for identifying microbes in various environmental samples without the need for first culturing the microbes … More Metagenomics for identification of microbes

Utility of rescue experiments in biology

Loss of function assays are common in biology for understanding the function associated with a protein or gene. Typically, targeted mutagenesis is used for creating a specific gene or protein mutant, that due to loss of critical sequence information, result in a loss of function. Thus, the function lost can be associated with the gene … More Utility of rescue experiments in biology

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

Long flight tube in time-of-flight mass spectrometer enables better separation of different analyte ions

Molecular ions literally fly through the flight tube of the time-of-flight mass spectrometer where at the end of the travel, they are detected as an electrical charge on the detector. The duration of flight was measured and is a key parameter for calculation of the mass/charge ratio of the molecular ion based on a calibration … More Long flight tube in time-of-flight mass spectrometer enables better separation of different analyte ions

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

Is there a theoretical mass limit to MALDI-TOF mass spectrometry?

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) uses a laser to ionize molecules from a matrix coated sample surface, accelerate them along a vacuum tube through the application of an electric field, and obtained a mass/charge ratio of the molecular ion by timing the flight of the ion. Given that time-of-flight of the molecular … More Is there a theoretical mass limit to MALDI-TOF mass spectrometry?

How do we obtain structural information of protein?

Readers would often find scientific papers describing the structure of a single protein or molecule. However, given that we do not have the capability of manipulating single protein or molecule with ease, how do we image a single protein or molecule to obtain its structural information?   The answer lies in the use of X-ray … More How do we obtain structural information of protein?

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

Need for proteome molecular mass library to aid peak identification in MALDI-TOF MS microbial identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) generates microorganism-specific mass spectrum which has been shown to be useful in microbial identification via the mass spectrum fingerprinting approach. Specifically, the mass spectrum of an unknown microorganism is compared against those catalogued in a reference database of known microbes to aid in positive identification of microbe. … More Need for proteome molecular mass library to aid peak identification in MALDI-TOF MS microbial identification

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