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Recent Research Papers of Note in Proteomics: Jun 5, 2008

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Journal: Rapid Communications in Mass Spectrometry: RCM, June
Title: Lys Tag: An easy and robust chemical modification for improved de novo sequencing with a matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometer
Authors: P Conrotto; U Hellman
 
Described is a method of “fast, efficient, and cheap lysine derivatization” for the purposes of de novo sequencing of peptides and proteins. The method improves the signals from lysine-terminated peptides and can be used to block lysine in combination with other derivatization methods, the authors said in the abstract. “Most importantly, upon peptide fragmentation it generates a neat series of predominantly y-ions, allowing the determination of unambiguous amino acid sequences,” they said.
 

 
Journal: Molecular & Cellular Proteomics, May 31 [Epub ahead of print]
Title: Generalized method for probability-based peptide and protein identification from tandem mass spectrometry data and sequence database searching
Authors: A Ramos-Fernandez; A Paradela; R Navajas; JP Albar
 
Authors used generalized lambda distributions to model frequency distributions of database search scores computed by Mascot, X!Tandem with k-score plug-in, OMSSA, and InsPecT to estimate p-values and false discovery rates with “high accuracy,” according to the abstract.
 
From the set of peptide assignments from the search engines, they defined a generic protein scoring scheme “that enabled accurate estimation of protein-level p-values by simulation of random score distributions, which was also found to yield good estimates of protein-level,” false discovery rates, the authors said in the abstract.
 

 
Journal: Analytical Chemistry, May 31 [Epub ahead of print]
Title: Fluorescein as a versatile tag for enhanced selectivity in analyzing cysteine-containing proteins/peptides using mass spectrometry
Authors: SH Chen; JL Hus; FS Lin
 
Authors report a novel cysteinyl tagging method using a fluorescein derivative. Such dyes have been shown to have multiple unique characteristics such as a unique reporter ion containing the dye moiety caused by collision-induced dissociation and high affinity toward multicarboxylate functional groups, “which could be useful for enhanced selectivity in MS-based proteomics,” according to the abstract.
 

 
Journal: Journal of Proteome Research, May 31 [Epub ahead of print]
Title: Increased throughput and reduced carryover of mass spectrometry-based proteomics using a high-efficiency nonsplit nanoflow parallel dual-column capillary HPLC system
Authors: H Wang; SM Hanash
 
Authors report a fully automated, high-efficiency parallel nonsplit nanoflow capillary system, coupled on-line with a linear ion trap and high performance nanoelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The system is intended for high-throughput proteomic analysis of complex mixtures, such as serum and plasma. It consists of two reversed-phase trap columns and two reversed-phase analytical capillary columns.
 

 
Journal: Molecular & Cellular Proteomics, May 29 [Epub ahead of print]
Title: Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer
Authors: M Bantscheff; M Boesche; D Eberhard; T Matthieson; G Sweetman; B Kuster
 
Authors show that by optimizing instrument parameters such as collision energy, activation Q, delay time, ion isolation width, the number of microscans, and number of trapped ions, low mass-to-charge ratio fragment ion intensities can be generated that enable accurate peptide quantification at the 100-attomolar level. The paper also gives “practical guidance for the implementation of PQD, discusses its merits and, for the first time, compares its performance to HCD,” according to the abstract.
 

 
Journal: Journal of Proteome Research, May 28 [Epub ahead of print]
Title: Rapid and accurate peptide identification from tandem mass spectra
Authors: CY Park; AA Clark; IL Ka; MJ MacCoss; WS Noble
 
Described is a database search engine called Crux that the authors say re-implements and extends Sequest. Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. It also implements two recently published post-processing methods: a p value calculation based on a Weibull distribution to the observed scores, and a semi-supervised method that “learns to discriminate between target and decoy matches,” according to the abstract. Crux is implemented in C and distributed with source code to non-commercial users freely.
 

 
Journal: Nature Biotechnology, May 25 [Epub ahead of print]
Title: Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
Authors: O Schilling; CM Overall
 
The authors identified endprotease cleavage sites by using peptides in peptide libraries with protected primary amines “to simultateneously determine sequence preferences on the N-terminal and C-terminal sides of the scissile bond,” they said in the abstract. P-terminal side cleave products were tagged with biotin, isolated and identified b tandem mass spectrometry, and the corresponding C-terminal side sequences were derived from human proteome databases using bioinformatics.
 

 
Journal: Electrophoresis, May 21 [Epub ahead of print]
Title: Sample complexity reduction for two-dimensional electrophoresis using solution isoelectric focusing prefractionation
Authors: MR Richardson, S Liu; HN Ringham; V Chan; FA Witzmann
 
According to the authors, 2-DE is of limited use for the analysis of cellular proteomes where fewer than 2,000 protein spots are frequently detected on a single 2-D gel. To overcome this, they used solution isoelectric focusing via the Xoom IEF Fractionator to generate sample fractions from complex bacterial lysates. They then did parallel 2-DE using narrow IPG strips that bracket the isoelectric focusing fractions. The result was a “significant enrichment of the bacterial proteome resolved on multiple 2-D gels,” according to the abstract. After prefractionation, they detected 5,525 spots, or about a 3.5-fold increase over the 1,577 spots detected in an unfractionated gel.
 

 
Journal: Journal of Proteome Research, May 20 [Epub ahead of print]
Title: Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells
Authors: W Dormeyer; D van Hoof; SR Braam; AJ Heck; CL Mummery; J Krijgsveld.
 
Presented is a strategy for identifying plasma membrane proteins optimized for application to the relatively small numbers of stem cells normally available and that does not require cell fractionation. Using their method, the authors identified 237 and 219 specific plasma membrane proteins in the hESC line HUES-7 and hECC line NT2/D1, respectively.
 

 
Journal: Journal of Proteome Research, May 20 [Epub ahead of print]
Title: Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells
Authors: B de Roos, SJ Duthie; C Polley; F Mulholland; FG Bouwman; C Heim; GJ Rucklidge; IT Johnson; EC Mariman; H Daniel; RM Elliott
 
Authors set out to design, optimize, and validate protocols for blood processing prior to proteomic analysis of plasma, platelets, and peripheral blood mononuclear cells, and to determine analytical variation of a single sample of depleted plasma, platelet, and PBMC proteins within and between four laboratories that used their own SOPs for two-dimensional gel electrophoresis.
 

 
Journal: Molecular & Cellular Proteomics, May 18 [Epub ahead of print]
Title: A multiplexed quantitative strategy for membrane proteomics: Opportunities for mining therapeutic targets for autosomal-dominant polycystic kidney disease
Authors: CL Han; CW Chien; WC Chen; YR Chen; CP Wu; H Li; YJ Chen
 
Authors describe a strategy combining gel-assisted digestion, iTRAQ labeling, and LC-MS/MS for a multiplexed, comprehensive, and robust quantitation of the membrane proteome. Using their method, they report being able to quantitate as many as 520 membrane proteins, each quantified based on an average of 14.1 peptides per integral membrane protein.
 

 
Journal: Nucleic Acids Research, May 15 [Epub ahead of print]
Title: PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation
Authors: S Montgomerie; JA Cruz; S Shrivastava; D Arndt; M Berjanskii; DS Wishart
 
Authors describe PROTEUS2, a web server designed “to support comprehensive protein structure prediction and structure-based annotation,” according to the abstract. PROTEUS2 accepts single or multiple sequences, and predicts the secondary and, if possible, tertiary structure of the query protein. Unlike most other tools or servers, the authors said, PROTEUS2 bundles signal peptide identification, transmembrane heli prediction, transmembrane beta-strand prediction, secondary structure prediction, and homology modeling into a single prediction pipeline.
 

 
Journal: Analytical Chemistry, May 15 [Epub ahead of print]
Title: Exploring the precursor ion exclusion feature of liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry for improving protein identification in shotgun proteome analysis
Authors: N Wang; L Li
 
Authors explore precursor ion exclusion in an electrospray ionization quadrupole time-of-flight mass spectrometer as a method for mitigating undersampling in shotgun proteome analysis by LC-MS/MS. The strategy is based on running replicates of the sample where the precursor ions detected in the initial runs are excluded for MS/MS in the subsequent run.

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