Detecting differential and correlated protein expression in label-free shotgun proteomics

B Zhang, NC VerBerkmoes, MA Langston… - Journal of proteome …, 2006 - ACS Publications
Recent studies have revealed a relationship between protein abundance and sampling
statistics, such as sequence coverage, peptide count, and spectral count, in label-free liquid …

Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress

D Bhushan, A Pandey, MK Choudhary, A Datta… - Molecular & Cellular …, 2007 - ASBMB
Water deficit or dehydration is the most crucial environmental factor that limits crop
productivity and influences geographical distribution of many crop plants. It is suggested that …

Glucose-dependent de novo lipogenesis in B lymphocytes: a requirement for atp-citrate lyase in lipopolysaccharide-induced differentiation

FJ Dufort, MR Gumina, NL Ta, Y Tao, SA Heyse… - Journal of Biological …, 2014 - ASBMB
Bacterially derived lipopolysaccharide (LPS) stimulates naive B lymphocytes to differentiate
into immunoglobulin (Ig)-secreting plasma cells. Differentiation of B lymphocytes is …

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics

P Mortensen, JW Gouw, JV Olsen, SE Ong… - Journal of proteome …, 2010 - ACS Publications
Mass spectrometry-based proteomics critically depends on algorithms for data interpretation.
A current bottleneck in the rapid advance of proteomics technology is the closed nature and …

Amino acid-coded tagging approaches in quantitative proteomics

X Chen, L Sun, Y Yu, Y Xue, P Yang - Expert review of proteomics, 2007 - Taylor & Francis
To improve the efficiency, accuracy, reproducibility, throughput and proteome coverage of
mass spectrometry-based quantitative approaches, both in vitro and in vivo tagging of …

Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.)

A Pandey, S Chakraborty, A Datta… - Molecular & cellular …, 2008 - ASBMB
Dehydration or water-deficit is one of the most important environmental stress factors that
greatly influences plant growth and development and limits crop productivity. Plants respond …

Proteome research based on modern liquid chromatography–tandem mass spectrometry: separation, identification and quantification

T Fröhlich, GJ Arnold - Journal of Neural Transmission, 2006 - Springer
Recent developments of new generations of mass spectrometers and improvements in the
field of chromatography have revolutionized protein analytics. Particularly the combination of …

Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells

RD Unwin, DL Smith, D Blinco, CL Wilson, CJ Miller… - Blood, 2006 - ashpublications.org
The proteome is determined by rates of transcription, translation, and protein turnover.
Definition of stem cell populations therefore requires a stem cell proteome signature …

Quantitative circadian phosphoproteomic analysis of Arabidopsis reveals extensive clock control of key components in physiological, metabolic, and signaling …

MK Choudhary, Y Nomura, L Wang… - Molecular & Cellular …, 2015 - ASBMB
The circadian clock provides adaptive advantages to an organism, resulting in increased
fitness and survival. The phosphorylation events that regulate circadian-dependent …

Dehydration-responsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation, and evolutionary perspective

MK Choudhary, D Basu, A Datta, N Chakraborty… - Molecular & Cellular …, 2009 - ASBMB
Water deficit or dehydration is the most crucial environmental constraint on plant growth and
development and crop productivity. It has been postulated that plants respond and adapt to …