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In Print: Recent Proteomics Papers of Note: Sep 21, 2012

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In Print: Recent Proteomics Papers of Note

Journal: Blood, August 6 [Epub ahead of print]

Title: The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways.

Authors: Burkhart JM; Vaudel M; Gambaryan S; Radau S; Walter U; Martens L; Geiger J; Sickmann A; Zahedi RP.

The authors created the first comprehensive, quantitative profile of the human platelet proteome, identifying roughly 4,000 proteins of which they estimated copy numbers for 3,700. This data, they wrote, allows an appraisal of protein networks and pathways in human platelets, providing a starting point for disease-oriented platelet proteomics.


Journal: Diabetes, August 7 [Epub ahead of print]

Title: Urinary proteomics for early diagnosis in diabetic nephropathy.

Authors: Zürbig P; Jerums G; Hovind P; Macisaac R; Mischak H; Nielsen SE; Panagiotopoulos S; Persson F; Rossing P.

The authors used mass spec to develop protein profiles in urine capable of detecting progression to macroalbuminuria in normoalbuminuric subjects up to five years in advance of symptoms with area under the curve of .93.


Journal: PLoS One, August 8 [Epub ahead of print]

Title: Mathematical modeling of the MAP kinase pathway using proteomic datasets.

Authors: Tian T; Song J.

The authors describe a computational system for mathematical modeling of complex cell signaling pathways. Using the MAP kinase pathway as a test system, they developed a model of this network in good agreement with experimental observations.


Journal: International Journal of Mass Spectrometry, August 10 [Epub ahead of print]

Title: Identification of phosphorylated human peptides by accurate mass measurement alone.

Authors: Mao Y; Zamdborg L; Kelleher NL; Hendrickson CL; Marshall AG.

The authors presented research finding that with high enough mass accuracy, phosphorylated peptides can be distinguished from unmodified peptides by mass alone, raising the possibility of online LC MS/MS systems that identify phosphopeptide precursors in MS1 for dissociation in MS2 to identify the peptide and phosphosite.


Journal: Molecular & Cellular Proteomics, August 20 [Epub ahead of print]

Title: Proteomic characterization of phagosomal membrane microdomains during phagolysosome biogenesis and evolution.

Authors: Goyette G; Boulais J; Carruthers NJ; Landry CR; Jutras I; Duclos S; Dermine JF; Michnick SW; Laboissière S; Lajoie G; Barreiro L; Thibault P; Desjardins M.

The authors used a proteomic analysis to analyze the association of proteins to various membrane microdomains in maturing phagosomes, finding evidence to support models of phagosome maturation involving the reorganization of the proteome by coordinated spatial segregation of proteins.


Journal:Analytical Chemistry, August 20 [Epub ahead of print]

Title: Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses.

Authors: McAlister GC; Huttlin EL; Haas W; Ting L; Jedrychowski MP; Rogers JC; Kuhn K; Pike I; Grothe RA; Blethrow JD; Gygi SP.

The authors present a method for increasing the throughput of TMT isobaric tags from 6-plex to 8-plex based on the ability of modern mass spectrometers to resolve small isotopic shifts. The technique, they note, could enable multiplexing up to 18-plex.


Journal: PLoS One, August 28 [Epub ahead of print]

Title: Identification of thalidomide-specific transcriptomics and proteomics signatures during differentiation of human embryonic stem cells.

Authors: Meganathan K; Jagtap S; Wagh V; Winkler J; Gaspar JA; Hildebrand D; Trusch M; Lehmann K; Hescheler J; Schlüter H; Sachinidis A.

The authors used tandem mass spectrometry to profile changes in human embryonic stem cells in response to thalidomide toxicity, identifying differential expression of limb, heart, and embryonic development related transcription factors and biological processes.


Journal: Proteomics Clinical Applications, August 28 [Epub ahead of print]

Title: Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures.

Authors: Sandström A; Andersson R; Segersvärd R; Löhr ZM; Borrebaeck CA; Wingren C.

Using recombinant antibody microarrays, the authors profiled the serum proteomes of 113 patients with pancreatitis as well as healthy controls, developing panels that could distinguish been different forms of pancreatitis and between cases and healthy controls.


Journal: Molecular & Cellular Proteomics, August 31 [Epub ahead of print]

Title: Biochemical fractionation and stable isotope dilution liquid chromatography-mass spectrometry for targeted and microdomain-specific protein quantification in human postmortem brain tissue.

Authors: Macdonald ML; Ciccimaro E; Prakash A; Banerjee A; Seeholzer SH; Blair IA; Hahn CG.

The authors developed a selected-reaction monitoring mass spec reaction for quantifying proteins and posttranslational modifications at the synapse using stable isotope-labeled proteome standard prepared with brain tissue of a labeled mouse. Using the developed assays they quantified more than 100 synaptic proteins and expect ultimately to be able to quantify more than 1,000.


Journal: Journal of Proteome Research, August 31 [Epub ahead of print]

Title: Mass spectrometry (LC-MS/MS) identified proteomic biosignatures of breast cancer in proximal fluid.

Authors: Whelan SA; He J; Lu M; Souda P; Saxton R; Faull KF; Whitelegge JP; Chang H.

The researchers describe an early biomarker discovery project using LC-MS/MS to identify serum protein markers in three clinically important types of breast cancer. They detected 249 proteins in the proximal fluid of seven breast cancer cell lines and developed signatures capable of categorizing the lines as either HER2 positive, HER2 negative and HR positive, or triple negative.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.