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Benjamín J Sánchez et al.
Proteomics, 21(6), e2000093-e2000093 (2021-01-17)
Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for predicting genome-wide absolute protein abundances. A known caveat of this approach, however, is the poor technical reproducibility, that is, how consistent predictions are when the same
Mari J Aaltonen et al.
The Journal of cell biology, 213(5), 525-534 (2016-06-01)
Mitochondria exert critical functions in cellular lipid metabolism and promote the synthesis of major constituents of cellular membranes, such as phosphatidylethanolamine (PE) and phosphatidylcholine. Here, we demonstrate that the phosphatidylserine decarboxylase Psd1, located in the inner mitochondrial membrane, promotes mitochondrial
Lee Dicker et al.
Molecular & cellular proteomics : MCP, 9(12), 2704-2718 (2010-09-09)
Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics provides a wealth of information about proteins present in biological samples. In bottom-up LC-MS/MS-based proteomics, proteins are enzymatically digested into peptides prior to query by LC-MS/MS. Thus, the information directly available from the LC-MS/MS
Kotaro Chihara et al.
RNA (New York, N.Y.) (2022-11-04)
New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar
Rosemary Yu et al.
Nature communications, 11(1), 1881-1881 (2020-04-22)
Cells maintain reserves in their metabolic and translational capacities as a strategy to quickly respond to changing environments. Here we quantify these reserves by stepwise reducing nitrogen availability in yeast steady-state chemostat cultures, imposing severe restrictions on total cellular protein and
Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A, et al.
Molecular and Cellular Proteomics, 13, 1925-1925 (2014)
Minia Antelo-Varela et al.
Frontiers in bioengineering and biotechnology, 8, 143-143 (2020-03-19)
Bacillus subtilis has been extensively used as a microbial cell factory for industrial enzymes due to its excellent capacities for protein secretion and large-scale fermentation. This bacterium is also an attractive host for biopharmaceutical production. However, the secretion potential of
Jacek R Wiśniewski et al.
Molecular systems biology, 8, 611-611 (2012-09-13)
We report a proteomic analysis of microdissected material from formalin-fixed and paraffin-embedded colorectal cancer, quantifying > 7500 proteins between patient matched normal mucosa, primary carcinoma, and nodal metastases. Expression levels of 1808 proteins changed significantly between normal and cancer tissues
Arne H Smits et al.
Nucleic acids research, 42(15), 9880-9891 (2014-07-25)
While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass
Jenny Forshed et al.
Molecular & cellular proteomics : MCP, 10(10), M111-M111 (2011-07-08)
We present a tool to improve quantitative accuracy and precision in mass spectrometry based on shotgun proteomics: protein quantification by peptide quality control, PQPQ. The method is based on the assumption that the quantitative pattern of peptides derived from one
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
Chang C, et al.
Bioinformatics, 35, 898-900 (2018)
Daniel Ruderman
Methods in molecular biology (Clifton, N.J.), 1550, 271-288 (2017-02-12)
Because proteomics experiments are so complex they can readily fail, and do so without clear cause. Using standard experimental design techniques and incorporating quality control can greatly increase the chances of success. This chapter introduces the relevant concepts and provides
Abida Sultan et al.
Frontiers in microbiology, 12, 657562-657562 (2021-04-24)
Understanding phosphorylation-mediated regulation of metabolic enzymes, pathways, and cell phenotypes under metabolic shifts represents a major challenge. The kinases associated with most phosphorylation sites and the link between phosphorylation and enzyme activity remain unknown. In this study, we performed stable
Liisa Arike et al.
Methods in molecular biology (Clifton, N.J.), 1156, 213-222 (2014-05-06)
Label-free proteome quantification methods used in bottom-up mass-spectrometry based proteomics are gaining more popularity as they are easy to apply and can be integrated into different workflows without any extra effort or cost. In the label-free proteome quantification approach, samples
Christina Ludwig et al.
Molecular & cellular proteomics : MCP, 11(3), M111-M111 (2011-11-22)
For many research questions in modern molecular and systems biology, information about absolute protein quantities is imperative. This information includes, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes, or quantitative comparisons of different proteins
Jianqiu Zhang et al.
BMC genomics, 11 Suppl 3, S8-S8 (2010-12-22)
The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise and
Jens Hör et al.
The EMBO journal, 39(9), e103852-e103852 (2020-04-01)
RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNA-protein complexes in Gram-positive species
Philip J Jackson et al.
Photosynthesis research, 155(3), 219-245 (2022-12-22)
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis
Minia Antelo-Varela et al.
Analytical chemistry, 91(18), 11972-11980 (2019-08-20)
The field of systems biology has been rapidly developing in the past decade. However, the data produced by "omics" approaches is lagging behind the requirements of this field, especially when it comes to absolute abundances of membrane proteins. In the
Iván Domenzain et al.
Nature communications, 13(1), 3766-3766 (2022-07-01)
Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of
Ozren Bogdanović et al.
Nature genetics, 48(4), 417-426 (2016-03-02)
The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage. However, the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of
Qi Qi et al.
mBio, 11(6) (2020-11-12)
Protein folding is often considered the flux controlling process in protein synthesis and secretion. Here, two previously isolated Saccharomyces cerevisiae strains with increased α-amylase productivity were analyzed in chemostat cultures at different dilution rates using multi-omics data. Based on the
Andrew F Jarnuczak et al.
Journal of proteome research, 15(9), 2945-2959 (2016-07-28)
Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from
V S Skvortsov et al.
Biomeditsinskaia khimiia, 63(4), 341-350 (2017-09-02)
Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) ("Sigma-Aldrich", USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS
Jan Muntel et al.
Journal of proteome research, 18(3), 1340-1351 (2019-02-07)
Label-free quantification (LFQ) and isobaric labeling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT SPS/MS3 10-plex workflow to a label free single shot data-independent acquisition (DIA) workflow on a controlled
Qi Wu et al.
The Analyst, 139(1), 138-146 (2013-11-07)
Proteome scale absolute quantification is fundamental for the quantitative understanding of an organism. The unsatisfactory accuracy for protein abundance estimation of current algorithms has been partially improved by the Absolute Protein EXpression profiling (APEX) algorithm, which implements the prior expectations
Jutta Brendel et al.
The Journal of biological chemistry, 289(10), 7164-7177 (2014-01-25)
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the
Boumediene Soufi et al.
Frontiers in microbiology, 6, 103-103 (2015-03-06)
We set out to provide a resource to the microbiology community especially with respect to systems biology based endeavors. To this end, we generated a comprehensive dataset monitoring the changes in protein expression, copy number, and post translational modifications in
Erik Ahrné et al.
Proteomics, 13(17), 2567-2578 (2013-06-25)
There is a great interest in reliable ways to obtain absolute protein abundances at a proteome-wide scale. To this end, label-free LC-MS/MS quantification methods have been proposed where all identified proteins are assigned an estimated abundance. Several variants of this
Muaaz Gul Awan et al.
Bioinformatics (Oxford, England), 32(10), 1518-1526 (2016-01-24)
Modern proteomics studies utilize high-throughput mass spectrometers which can produce data at an astonishing rate. These big mass spectrometry (MS) datasets can easily reach peta-scale level creating storage and analytic problems for large-scale systems biology studies. Each spectrum consists of
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