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In Print: Last Month's Proteomics Papers of Note: Nov 4, 2011


Proteomics Research Papers of Note, September and October 2011

Journal: Molecular & Cellular Proteomics, Sept. 1 [Epub ahead of print]

Title: A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.

Authors: Wagner SA; Beli P; Weinert BT; Nielsen ML; Cox J; Mann M; Choudhary C.

The researchers mapped 11,054 endogenous putative ubiquitylation sites on 4,273 human proteins using a single-step immunoenrichment of ubiquitylated peptides followed by high-resolution mass spec. They also quantified global ubiquitylation in cells treated with the proteasome inhibitor MG-132 to identify sites involved in proteasomal degradation.

Journal: Nature Methods, Sept. 4

Title: Firefly luciferase mutants as sensors of proteome stress.

Authors: Gupta R; Kasturi P; Bracher A; Loew C; Zheng M; Villella A; Garza D; Hartl FU; Raychaudhuri S.

The researchers describe the use of EGFP-tagged proteins for the comparative measurement of proteostasis capacity in a variety of cell types and organisms.

Journal: Proteomics, Sept. 7 [Epub ahead of print]

Title: An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates.

Authors: Ahrné E; Ohta Y; Nikitin F; Scherl A; Lisacek F; Müller M.

The researchers present a new method for the construction of decoy peptide MS/MS spectra that uses new techniques to prevent decoy spectra from being too similar to original library spectra while keeping intact important features of real MS/MS data.

Journal: Molecular & Cellular Proteomics, Sept. 13 [Epub ahead of print]

Title: Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics.

Authors: Jedrychowski MP; Huttlin EL; Haas W; Sowa ME; Rad R; Gygi SP.

The researchers compare higher energy collisional dissociation to collision-induced dissociation for large-scale phosphorylation analyses of murine brain, finding that CID fragmentation provides substantially richer datasets but that HCD shows promise for the future.

Journal: PLoS One, Sept. 14 [Epub ahead of print]

Title: Proteomic interrogation of human chromatin.

Authors: Torrente MP; Zee BM; Young NL; Baliban RC; LeRoy G; Floudas CA; Hake SB; Garcia BA.

The researchers used mass spectrometry to identify proteins in selected chromatin preparations and produced a chromatin catalog, including proteins ranging from highly abundant histones to less abundant members of other chromatin machinery complexes. They quantified the relative abundances of these proteins across the different fractions and investigated their post-translational modifications.

Journal: Molecular & Cellular Proteomics, Sept. 21 [Epub ahead of print]

Title: A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling.

Authors: Guan S; Price JC; Prusiner SB; Ghaemmaghami S; Burlingame AL.

The authors present a data processing pipeline consisting of a suite of software modules required to reduce large sets of LC-MS/MS data into protein turnover rate constant for proteome dynamics studies.

Journal: Cell, Sept. 29 [Epub ahead of print]

Title: Global Identification of Modular Cullin-RING Ligase Substrates.

Authors: Emanuele MJ; Elia AE; Xu Q; Thoma CR; Izhar L; Leng Y; Guo A; Chen YN; Rush J; Hsu PW; Yen HC; Elledge SJ.

Using genetic and proteomic assays the researchers identified hundreds of proteins regulated by Cullin-RING ligases, the largest E3 ubiquitin ligase family in eukaryotes, demonstrating the broad role of CRL ubiquitylation in cellular biology and identifying proteins likely to be key indicators of cellular physiology.

Journal: Journal of Proteomics, Oct. 8 [Epub ahead of print]

Title: CysTRAQ — A combination of iTRAQ and enrichment of cysteinyl peptides for uncovering and quantifying hidden proteomes.

Authors: Tambor V; Hunter CL; Seymour SL; Kacerovsky M; Stulik J; Lenco J.

The researchers present a new technique enabling iTRAQ-based quantitation of peptides based on the presence of cysteine residues.

Journal: Molecular & Cellular Proteomics, Oct. 11 [Epub ahead of print]

Title: 18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry.

Authors: Kim JS; Fillmore TL; Liu T; Robinson E; Hossain M; Champion BL; Moore RJ; Camp DG 2nd; Smith RD; Qian WJ.

The authors present a proof-of-concept study using an 18O-labeled proteome reference as internal standards for selected reaction-monitoring mass spectrometry, providing a potential alternative to expensive stable isotope-labeled synthetic peptides for large-scale SRM experiments.

Journal: Molecular Systems Biology; Oct. 11

Title: Toward an understanding of the protein interaction network of the human liver.

Authors: Wang J; Huo K; Ma L; Tang L; Li D; Huang X; Yuan Y; Li C; Wang W; Guan W; Chen H; Jin C; Wei J; Zhang W; Yang Y; Liu Q; Zhou Y; Zhang C; Wu Z; Xu W; Zhang Y; Liu T; Yu D; Zhang Y; Chen L; Zhu D; Zhong X; Kang L; Gan X; Yu X; Ma Q; Yan J; Zhou L; Liu Z; Zhu Y; Zhou T; He F; Yang X.

The researchers detail a yeast two-hybrid protein interaction map covering the interactions of an unbiased set of 5,026 human liver proteins, establishing a human liver protein interaction network composes of 3,484 interactions among 2,582 proteins.

Journal: Clinical Chemistry, Oct 13 [Epub ahead of print]

Title: The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid.

Authors: Rosenling T; Stoop MP; Smolinska A; Muilwijk B; Coulier L; Shi S; Dane A; Christin C; Suits F; Horvatovich PL; Wijmenga SS; Buydens LM; Vreeken R; Hankemeier T; van Gool AJ; Luider TM; Bischoff R.

The authors investigated the impact of delayed storage on the proteome and metabolome of cerebrospinal fluid to determine if current sample handling for CSF in the clinic is adequate. They found that the measured proteome and metabolome in CSF is stable at room temperature for up to two hours.

Journal: Proceedings of the National Academy of Sciences, Oct. 17 [Epub ahead of print]

Title: Physical limits of cells and proteomes.

Authors: Dill KA; Ghosh K; Schmit JD.

The authors present a model combining known protein sizes, stabilities, and rates of folding and diffusion with the know protein-length distributions of several proteomes to address questions of cell physics and the physical limits of cell behavior.

Journal: Journal of Proteomics, Oct. 20 [Epub ahead of print]

Title: Harry Belafonte and the secret proteome of coconut milk.

Authors: D'Amato A; Fasoli E; Righetti PG.

The researchers mapped the proteome of coconut milk, identifying 307 unique gene products using combinatorial peptide ligand libraries.

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

Title: Antibody-based protein profiling of the human chromosome 21.

Authors: Uhlén M; Oksvold P; Algenas C; Hamsten C; Fagerberg L; Klevebring D; Lundberg E; Odeberg J; Pontén F; Kondo T; Sivertsson A.

As part of the Human Proteome Project the authors undertook a systematic analysis of chromosome 21 using an antibody-based approach for protein profiling. They present a chromosome-wide matrix with status for all chromosome 21 genes regarding subcellular localization, tissue distribution, and molecular characterization of the corresponding proteins.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.