The ABC's (and XYZ's) of peptide sequencing
Proteomics is an increasingly powerful and indispensable technology in molecular cell
biology. It can be used to identify the components of small protein complexes and large …
biology. It can be used to identify the components of small protein complexes and large …
Proteomics: the first decade and beyond
SD Patterson, RH Aebersold - Nature genetics, 2003 - nature.com
Proteomics is the systematic study of the many and diverse properties of proteins in a
parallel manner with the aim of providing detailed descriptions of the structure, function and …
parallel manner with the aim of providing detailed descriptions of the structure, function and …
[HTML][HTML] Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis
R Zarnowski, H Sanchez, AS Covelli, E Dominguez… - PLoS …, 2018 - journals.plos.org
Cells from all kingdoms of life produce extracellular vesicles (EVs). Their cargo is protected
from the environment by the surrounding lipid bilayer. EVs from many organisms have been …
from the environment by the surrounding lipid bilayer. EVs from many organisms have been …
A statistical model for identifying proteins by tandem mass spectrometry
AI Nesvizhskii, A Keller, E Kolker… - Analytical …, 2003 - ACS Publications
A statistical model is presented for computing probabilities that proteins are present in a
sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a …
sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a …
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
A Keller, AI Nesvizhskii, E Kolker… - Analytical …, 2002 - ACS Publications
We present a statistical model to estimate the accuracy of peptide assignments to tandem
mass (MS/MS) spectra made by database search applications such as SEQUEST …
mass (MS/MS) spectra made by database search applications such as SEQUEST …
Coordination of fungal biofilm development by extracellular vesicle cargo
The fungal pathogen Candida albicans can form biofilms that protect it from drugs and the
immune system. The biofilm cells release extracellular vesicles (EVs) that promote …
immune system. The biofilm cells release extracellular vesicles (EVs) that promote …
Trypsin cleaves exclusively C-terminal to arginine and lysine residues
Almost all large-scale projects in mass spectrometry-based proteomics use trypsin to convert
protein mixtures into more readily analyzable peptide populations. When searching peptide …
protein mixtures into more readily analyzable peptide populations. When searching peptide …
Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures
GZ Li, JPC Vissers, JC Silva, D Golick… - …, 2009 - Wiley Online Library
A novel database search algorithm is presented for the qualitative identification of proteins
over a wide dynamic range, both in simple and complex biological samples. The algorithm …
over a wide dynamic range, both in simple and complex biological samples. The algorithm …
Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry
Blood serum is a complex body fluid that contains various proteins ranging in concentration
over at least 9 orders of magnitude. Using a combination of mass spectrometry technologies …
over at least 9 orders of magnitude. Using a combination of mass spectrometry technologies …
PepNovo: de novo peptide sequencing via probabilistic network modeling
A Frank, P Pevzner - Analytical chemistry, 2005 - ACS Publications
We present a novel scoring method for de novo interpretation of peptides from tandem mass
spectrometry data. Our scoring method uses a probabilistic network whose structure reflects …
spectrometry data. Our scoring method uses a probabilistic network whose structure reflects …