Journal of Proteome Research

Metabonomics approach detects fetal abnormalities

Thu, 07 Jul 2009 10:00:00 EDT

Researchers identify metabolite changes in the amniotic fluid surrounding malformed fetuses, and this information could enhance our understanding and diagnosis of fetal disorders.

A compact, enrichable protein cross-linker

Thu, 30 Jun 2009 10:00:00 EDT

An amine-reactive cross-linker enables the click-based enrichment of cross-linked peptides before LC/MS/MS analysis.

New analysis seen as validating dinosaur proteomics study

Thu, 23 Jun 2009 10:00:00 EDT

John Asara, Mary Schweitzer, and colleagues follow up their controversial 2007 T. rex study with collagen sequenced from a different dinosaur.

Extracellular secreted antigens of malaria

Tue, 16 Jun 2009 12:00:00 EDT

Investigators identify erythrocyte-secreted P. falciparum proteins that might function in immune modulation and signaling.

Comparison of two large-scale methods for proteolytic mapping

Tue, 09 Jun 2009 12:00:00 EDT

Researchers demonstrate agreement and complementarity of the PROTOMAP and subtiligase approaches for the analysis of apoptotic proteolysis.

FFPE samples almost as good as frozen ones

Tue, 09 Jun 2009 12:00:00 EDT

Samples should be fixed with care and data sets merged before searches for protein identifications.

2D mass mapping for MS data visualization

Tue, 26 May 2009 12:00:00 EDT

New method eases the bottleneck of data representation in MS-based de novo peptide sequencing.

Decon2LS for high-resolution MS data

Tue, 26 May 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

PROTEOMER: a database for 2DE-centered proteomics

Tue, 26 May 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Enzymes associated with antibiotic resistance in MRSA

Tue, 19 May 2009 12:00:00 EDT

By comparing enzyme activities in antibiotic-sensitive and -resistant S. aureus strains, investigators discover resistance mechanisms and potential drug targets.

New method for complexome analysis

Tue, 19 May 2009 12:00:00 EDT

To fractionate protein complexes for downstream analysis, investigators combine two native gel electrophoresis techniques.

Protein–protein interactions shed light on blindness

Tue, 19 May 2009 12:00:00 EDT

By studying a protein’s interactome, researchers obtain hints at how a rare form of blindness may develop.

Infrared Fluorescent Protein Extends Imaging Range

Tue, 19 May 2009 12:00:00 EDT

An engineered protein that can be expressed in mammalian cells uses biliverdin as a chromophore, increasing the utility of fluorescent proteins

Sweetening the deal for fruit metabolomics

Tue, 12 May 2009 12:00:00 EDT

Correlation of 1H NMR and GC/ESI-TOFMS data sets enhances spatial metabolite analysis of melon.

New method identifies ADP-ribosylated proteins

Tue, 12 May 2009 12:00:00 EDT

Researchers use recently discovered macro domain to purify targets of ADP-ribosylation for MS identification.

Divining The Spliceosome

Tue, 12 May 2009 12:00:00 EDT

The missing link between humanity's small genome and huge proteome reveals some secrets

Proteomics of Chernobyl-grown seeds gives hints about adaptation to radiation

Tue, 05 May 2009 12:00:00 EDT

Martin Hajduch talks to JPR about conducting plant proteomics studies in the contaminated Chernobyl region of Ukraine.

Caffeine highs may lead to coral demise

Tue, 05 May 2009 12:00:00 EDT

Study suggests that caffeine in urban sewage effluent can alter protein expression in coral algae symbionts.

GC, LC, or CE: Which is best for quantitative metabolomics?

Tue, 05 May 2009 12:00:00 EDT

Researchers compare three chromatographic separation platforms for the MS analysis of 91 metabolites.

In Praise of Toolmakers

Tue, 05 May 2009 12:00:00 EDT

Editorial by Catherine Fenselau for the May 2009 issue.

The molecular face of prostate cancer

Tue, 28 Apr 2009 12:00:00 EDT

Toponomics finds unique protein combinations on cancer cells.

First characterization of CLPH, a spermatid-specific protein

Tue, 28 Apr 2009 12:00:00 EDT

Researchers analyze a novel phosphoprotein that likely functions in mammalian spermiogenesis.

Drosophila melanogaster PeptideAtlas

Tue, 28 Apr 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

POSTMan for posttranslational modifications

Tue, 28 Apr 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Pancreatic cancer biomarker compendium

Tue, 28 Apr 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Collisions or Electrons? Protein Sequence Analysis in the 21st Century

Tue, 21 Apr 2009 12:00:00 EDT

The way dissociation is carried out determines the upstream sample-handling process, whereas the spectral features that dissociation produces influence the downstream informatics obtained.

Proteomics hints at problems with preimplantation genetic diagnosis

Tue, 21 Apr 2009 12:00:00 EDT

Mice that have undergone PGD appear to have neurological defects.

Carbon nanotubes improve native PAGE resolution

Tue, 21 Apr 2009 12:00:00 EDT

The addition of carbon nanotubes to native PAGE gels boosts the detection of some proteins.

Mass Spec Sequences Venom Peptides

Tue, 21 Apr 2009 12:00:00 EDT

A new mass spectrometry strategy makes it easier to sequence venom peptides, a diverse set of disulfide-rich natural products that are difficult to characterize

HUPO members talk quantitation in Barbados

Tue, 14 Apr 2009 12:00:00 EDT

The next HUPO study may address quantitation.

News: Rites of (stem cell) passage

Tue, 07 Apr 2009 12:00:00 EDT

With 2DE and MS, researchers characterize proteomic changes that arise during mesenchymal stem cell passage.

Katie Cottingham reports from the U.S. HUPO Fifth Annual Conference-San Diego

Tue, 07 Apr 2009 12:00:00 EDT

The controversial move of including a standard operating procedure enabled CPTAC researchers to reduce variability.

Quantitative affinity purification

Tue, 07 Apr 2009 12:00:00 EDT

An AP workflow that provides quantitative interaction data for protein complexes is proposed.

Monitoring translation to assess protein production

Tue, 07 Apr 2009 12:00:00 EDT

Researchers develop a new translation-based method to figure out which proteins are made in vivo.

Hurry for your chance at NIH stimulus funding

Tue, 31 Mar 2009 12:00:00 EDT

New funding opportunities exist as a result of the U.S. stimulus package.

Finding antigen culprits in an occupational disease

Tue, 31 Mar 2009 12:00:00 EDT

Researchers identify antigenic proteins in a recently discovered bacterium that has been associated with an immune-mediated disease in metal-cutting workers.

ECD: not so random after all?

Tue, 31 Mar 2009 12:00:00 EDT

Electron capture dissociation ICR MS study of amphipathic peptides shows cleavage specificity.

Quantitative peptidomics provides behavioral insights

Tue, 31 Mar 2009 12:00:00 EDT

The levels of eight brain peptides distinguish various groups of foraging honeybees.

Phosphoproteomics: Miles To Go Before It’s Routine

Tue, 24 Mar 2009 12:00:00 EDT

Researchers see major technological advances but still have significant challenges to overcome.

Systems Biology Metabolic Modeling Assistant

Tue, 24 Mar 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Estimating retention time shifts in LC/MS

Tue, 24 Mar 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Corra, a computational framework and tools for LC/MS proteomics

Tue, 24 Mar 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

MitoMiner: a database for mitochondrial proteomics

Tue, 24 Mar 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

How do psychotropic drugs work?

Tue, 17 Mar 2009 12:00:00 EDT

Although psychotropic drugs are readily prescribed for the treatment of various psychiatric disorders, their mechanisms of action are not well understood. Researchers use metabolomics to find clues.

Freeze-drying does not alter the human plasma proteome

Tue, 17 Mar 2009 12:00:00 EDT

Study shows that lyophilized human plasma is very similar in protein composition and clotting capacity to fresh-frozen plasma.

hPDQ: pretty darn quick generation of verification assays?

Tue, 17 Mar 2009 12:00:00 EDT

Researchers propose the Human Proteome Detection and Quantitation project to develop specific, MS-based assays for biomarker verification.

CID-MS/MS and CID–MS³ for phosphoproteome analysis: a cautionary tale

Tue, 17 Mar 2009 12:00:00 EDT

New evidence indicates widespread gas-phase rearrangement and competing fragmentation reactions in phosphopeptides analyzed by CID-MS/MS and CID-MS³.

A common aquarium fish helps unlock the secrets of melanoma

Tue, 10 Mar 2009 12:00:00 EDT

Proteins involved in ROS defense and signal transduction were among those that were differentially regulated in melanomas compared with benign and normal tissues of platyfish.

The proteome of plasma membrane vesicles

Tue, 10 Mar 2009 12:00:00 EDT

A new method for the harvesting, purification, and proteomics analysis of PMVs enables the identification of many proteins unique to the plasma membrane.

A new technique for palmitoylation profiling

Tue, 10 Mar 2009 12:00:00 EDT

Study reveals first palmitoylome of human cells.

Nanotubes Resolve Serum Proteins

Tue, 10 Mar 2009 12:00:00 EDT

Adding functionalized carbon nanotubes to a polyacrylamide gel permits better electrophoresis separation of proteins in complex mixtures

Profiling tyrosine kinase activation in cancer

Tue, 03 Mar 2009 12:00:00 EDT

New bead-based assay identifies a potential target for glioblastoma therapy.

Enhanced coverage of the plasma membrane proteome

Tue, 03 Mar 2009 12:00:00 EDT

Gel-based MS approach increases the detection of hard-to-study IMPs.

Toward a better understanding of celiac disease

Tue, 03 Mar 2009 12:00:00 EDT

Rapid deamidation of glutamine residues on a given gluten peptide increases the chances that an immune response will be triggered in CD patients.

Predicting charges for ETD spectra

Tue, 03 Mar 2009 12:00:00 EDT

An interview with Paulo Carvalho at Scripps Research Institute.

Prequips: a platform for systems biology analysis of proteomic data

Tue, 24 Feb 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Predicting high-responding peptides for MRM

Tue, 24 Feb 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

PINA platform for PPIs

Tue, 24 Feb 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

MatrixDB

Tue, 24 Feb 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Proteomics of deep belly fat versus subcutaneous fat

Tue, 17 Feb 2009 12:00:00 EDT

Belén Peral talks to JPR about the proteomic differences between omental fat and subcutaneous fat.

Microfluidics for protein–protein interactions

Tue, 17 Feb 2009 12:00:00 EDT

A microfluidic platform allows researchers to test thousands of protein interactions simultaneously.

Confidence score for interactions

Tue, 17 Feb 2009 12:00:00 EDT

Researchers report a new way to determine whether a binary PPI is a true positive.

AOHUPO takes on membrane proteins

Tue, 17 Feb 2009 12:00:00 EDT

Participants in the AOHUPO MPI used a variety of methods to identify membrane proteins from a liver microsomal membrane fraction.

C&EN: Biomarker For Cancer Aggression

Tue, 17 Feb 2009 12:00:00 EDT

Metabolite in urine is linked to prostate cancer’s progress.

Human protein factory for in vitro proteomics

Tue, 10 Feb 2009 12:00:00 EDT

A human protein factory allows scientists to express and study human proteins in vitro.

Phosphorylation puts sperm in the mood

Tue, 10 Feb 2009 12:00:00 EDT

Analysis of proteome changes at the cell surface

Tue, 10 Feb 2009 12:00:00 EDT

A label-free, quantitative approach detects changes in the cell-surface proteome.

Shrimp study exposes mechanisms of innate immunity

Tue, 03 Feb 2009 12:00:00 EDT

Researchers use MS and RNA interference to identify a novel role for Ran GTPases in innate immunity.

Proteomics reveals that individual cells react differently to a drug

Tue, 03 Feb 2009 12:00:00 EDT

The dynamics of some proteins differ among seemingly identical cells after drug treatment.

Neural palmitoyl proteins identified

Tue, 03 Feb 2009 12:00:00 EDT

In a study of the rat neural palmitoyl proteome, investigators identify known and novel palmitoyl proteins, including one that may be involved in forming the synapse.

Decision tree algorithm for MS/MS fragmentation

Tue, 27 Jan 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Computational method predicts blood-secreted proteins

Tue, 27 Jan 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Predicting posttranslational modifications

Tue, 27 Jan 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

MRMaid

Tue, 27 Jan 2009 12:00:00 EDT

This Toolbox item describes an algorithm, database, or computational method for proteomics analyses.

Improved coverage of the plasma membrane glycoproteome

Wed, 21 Jan 2009 12:00:00 EDT

Investigators combine results from lectin-affinity chromatography and glycocapture approaches to increase the number of plasma membrane glycoproteins identified by LC/MS/MS.

NMR-based environmental metabolomics: an international comparison

Wed, 21 Jan 2009 12:00:00 EDT

Researchers compare ¹H-NMR metabolomics data sets acquired by labs in four countries that analyzed the same environmental samples.

Variability is low in some sample preparation methods

Wed, 21 Jan 2009 12:00:00 EDT

By Katie Cottingham

One gene, multiple proteins

Tue, 13 Jan 2009 12:00:00 EDT

Proteomics study confirms the genomewide expression of alternative protein isoforms.

PEG-based SIL of low-molecular-weight metabolites

Tue, 13 Jan 2009 12:00:00 EDT

New labeling method improves LC/MS quantification of amine-containing metabolites.

Sweetening glycoprotein processing

Tue, 13 Jan 2009 12:00:00 EDT

A one-stop reactor boosts efficiency while saving time and money.

Elastase increases sequence coverage of the phosphoproteome

Tue, 06 Jan 2009 12:00:00 EDT

The low-specificity protease elastase is highly complementary to trypsin for phosphorylation site analysis.

Proteome changes in Huntington’s disease

Tue, 06 Jan 2009 12:00:00 EDT

An integrated proteomics analysis reveals potential biomarkers in CSF from patients with Huntington’s disease.