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Recent Research Papers of Note : Apr 23, 2010

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Journal: Rapid Communications in Mass Spectrometry: RCM, May 15
Title: Characterizing protein glycosylation sites through higher-energy C-trap dissociation
Authors: ZM Sequ; Y Mechref

Despite advances in mass spectrometry, assigning glycosylation sites of glycoproteins remains a "very challenging analytical task," the authors said in the abstract. Here, they show that glycopeptide ions can be fragmented efficiently using the higher-energy c-trap dissociation feature of an LTQ Orbitrap instrument. "An attractive aspect of this dissociation option is the generation of distinct Y1 ions (peptide+GlcNAc), thus allowing unequivocal assignment of N-glycosylation sites of glycoproteins," according to the abstract. "The combination of the very informative collision-induced dissociation spectra acquired in the linear ion trap with the distinct features of HCD offers very useful information aiding in the characterization of the glycosylation sites of glycoproteins."


Journal: Rapid Communications in Mass Spectrometry: RCM, April 30
Title: Surface-activated chemical ionization time-of-flight mass spectrometry and labeling-free approach: two powerful tools for the analysis of complex plant functional proteome profiles
Authors: A Finiguerra; A Spadafora; D Filadoro; S Mazzuca

According to the abstract, surface-activated chemical ionization has become a widely used method for analyzing a range of different compounds because of its high sensitivity and effectiveness under different chromatographic conditions. The authors use SACI in conjunction with a highly selective quadrupole TOF mass analyzer to characterize a complex proteome pattern after separation by SDS-PAGE. Compared with data obtained by a micro-ESI approach, SACI "strongly" increased the number of detectable proteins, the authors said.


Journal: Cell Cycle, April 28 [Epub ahead of print]
Title: Roles of "junk phosphorylation" in modulating biomolecular associatin of phosphorylated proteins?
Authors: CS Tan; C Jørgense; R Linding

Sequence conservation analysis of recent proteome-wide phosphorylation data suggests that many previously unidentified phosphorylation sites are not well-conserved. As a result, it is believed that many of these sites are not functional. The assumption, however, is that protein phosphorylation modulates protein function through specific positions on a protein sequence. "Based on emerging understanding on phosphoregulation of cellular activities, we argue, with examples, that non-positionally conserved phosphorylation sites can very well be functional," the authors said in the abstract.


Journal: Proteomics, April 13 [Epub ahead of print]
Title: Estimating false discovery rates for peptide and protein identification using randomized databases
Authors: G Hather; R Higdon; A Bauman; E Kolker

Described is a "straightforward" isotonic regression-based method for estimating the cumulative false discovery rates and local false discovery rates of peptide identification. The method performed as well as other methods, according to the abstract, and has the advantages of being monotonic in the score, computationally simple, and independent of assumptions about score distributions.


Journal: Analytical Chemistry, April 12 [Epub ahead of print]
Title: Highly sensitive detection of protein toxins by surface plasmon resonance with biotinylation-based inline atom transfer radical polymerization amplification
Authors: Y Liu; J Jauw; MJ Linman; Q Cheng

Authors report a method to enhance detection sensitivity in surface plasmon resonance spectroscopy by coupling a polymerization initiator to a biospecific interaction and inducing inline atom transfer radical polymerization for amplifying SPR response.


Journal: Proteomics, April 12 [Epub ahead of print]
Title: Differential proteomic analysis using isotope-coded protein labeling strategies: comparison, improvements and application to simulated microgravity effect on Cupriavidus metallidurans CH34
Authors: B Leroy; C Rosier; V Erculisse; N Leys; M Mergeay; R Wattiez

ICPL is a recent non-isobaric technique for labeling primary amines in proteins. While ICPL overcomes some of the disadvantages found in other chemical labeling techniques, such as iTRAQ or ICAT, other studies have shown that more than 30 percent of proteins identified by regular ICPL "generally remain unquantified." The authors describe a modified version of ICPL that makes it possible to label and quantify all peptides in a sample. They call their method post-digest ICPL.


Journal: Molecular & Cellular Proteomics, April 10 [Epub ahead of print]
Title: Addressing accuracy and precision issues in iTRAQ quantitation
Authors: NA Karp; W Huber; PG Sadowski; PD Charles; SV Hester; KS Lilley

While iTRAQ-based mass spectrometry allows for the quantitative comparison of protein abundance, current data analysis techniques for iTRAQ "struggle to report reliable relative protein abundance estimates and suffer with problems of precision and accuracy," according to the abstract. The authors describe a method combining peptide measurements to give a robust protein estimate "even when the data for the protein are sparse or at low intensity."


Journal: Journal of Proteome Research, April 8 [Epub ahead of print]
Title: Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation
Authors: DM Botelho; MJ Wall; DB Vieira; S Fitzsimmons; F Liu; AA Doucette

The authors compare two proteomic workflows incorporating SDS for protein separation — SDS-PAGE coupled to LC-MS, and a solution separation platform, GELFrEE, for intact proteome prefractionation and identification. "Remarkable agreement in the number and type of identified proteins was obtained from these two separation platforms, validating the use of SDS in solution-phase proteome analysis," according to the abstract.

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Journal: Analytical Chemistry, April 7 [Epub ahead of print]
Title: A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies
Authors: L Yang; X Tang; CR Weisbrod; GR Munske; JK Eng; PD von Haller; NK Kaiser; JE Bruce

Presented is a proof-of-concept study using a novel photocleavable and mass spectrometry identifiable cross-linker, pcPIR, or photocleavable protein interaction reporter. pcPIR can be dissociated under UV irradiation either offline or online before being introduced to mass spectrometry. Different types of cross-links can be identified using the pcPIR mass relationships, "where the mass of cross-linked precursor equals the sum of the masses of the released products and reporter," according to the abstract.


Journal: Journal of Proteome Research, April 7 [Epub ahead of print]
Title: MUDE: A new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification
Authors: FR Cergueira; A Graber; B Schwikowski; C Baumgartner

According to the abstract, the target-decoy search strategy has proven to be very efficient for error estimation, but "little attention has been paid to the resulting sensitivity. Only two scores are normally used and thresholds are explored in a very simplistic way." Here, a multivariate decoy analysis is described "where many quality parameters are considered" and the analysis is treated "as an optimization problem for sensitivity maximization."


Journal: Journal of Proteome Research, April 5
Title: Optimizing performance of glycopeptide capture for plasma proteomics
Authors: FS Berven; R Ahmad; KR Clauser; SA Carr

According to the abstract, "selective capture of glycopolypeptides followed by release and analysis of the former glycosylation-site peptides has been shown to have promise for reducing the complexity of body fluids such as blood for biomarker discovery." In the study, the authors optimized a protocol based on the capture of polypeptides containing an N-linked carbohydrate from human plasma using commercially available magnetic beads coupled with hydrazide chemistry. The protocol was automated through the use of a KingFisher magnetic particle processor.


Journal: Journal of Proteome Research, April 5
Title: Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics
Authors: Y Fang; DP Robinson; LJ Foster

Authors compare the most popular methods for fractionating samples at the protein and peptide levels. They replicate all analyses "to provide estimates of the variability in the analyses and controlling precisely for instrument time dedicated to each analysis, as well as directly measuring the recovery of protein or peptide from each fractionation procedure," according to the abstract. SDS-PAGE is the most effective measure tested for maximum proteome coverage. "When considering the amount of material recovered after each fractionation procedure, solution-based IEF and SCX performed similarly, with approximately 80 percent of the input being recovered," the authors said in the abstract.


Journal: Proteomics, April
Title: Laser-induced liquid bead ion desorption-MS of protein complexes from blue-native gels, a sensitive top-down proteomic approach
Authors: L Sokolova; I Wittig; HD Barth; H Schägger; B Brutschy; U Brandt

Describes an experimental approach combining two methods for proteomic analysis of large membrane protein complexes — blue native electrophoresis and laser-induced liquid bead ion desorption MS. BNE was used to separate protein complexes, which were then eluted from the gel. LILBID mass spectrometry resulted in the masses of the constituents of the multiprotein complexes. "High sensitivity and small sample volumes required for LILBID MS resulted in low demands on sample quantity," according to the abstract, and eluate from a single band allowed the authors to assess the mass of an entire multiprotein complex and its subunits. They validated their method with mitochondrial NADH:ubiquinone reductase from Yarrowia lipolytica.


Journal: Journal of Proteome Research, March 30 [Epub ahead of print]
Title: Comparison of a protein-level and peptide-level labeling strategy for quantitative proteomics of synaptosomes using isobaric tags
Authors: O Engmann; J Campbell; KP Giese; AJ Thompson

Describes a comparison of protein-level labeling GeLC-MS/MS strategy with a peptide-level labeling 2D LC-MS/MS method, using mouse hippocampus synaptosomes and isobaric tandem mass tags. Among the results they observed was that protein-level labeling resulted in three times the identification of protein over peptide-level labeling, 697 versus 241, and twice as many proteins with labeled peptides, 480 versus 232. Their results "demonstrate that protein-level labeling combined with GeLC-MS/MS is an effective strategy for the multiplexed quantitation of synaptosomal preparations, and may be applicable to samples of a similar proteomic complexity and dynamic range of protein abundance," according to the abstract.


Journal: Molecular & Cellular Proteomics, March 27 [Epub ahead of print]
Title: Peptide identification from mixture tandem mass spectra
Authors: J Wang; J Perez-Santiago; JE Katz; P Mallick; N Bandeira

"The success of high-throughput proteomics hinges on the ability of computational methods to identify peptides from tandem mass spectra," the authors said in the abstract. "However, a common limitation of most peptide identification approaches is the nearly ubiquitous assumption that each MS/MS spectrum is generated from a single peptide." They propose a new computational approach for identifying mixture spectra generated from more than one peptide. Their approach is able to identify up to 98 percent of all mixture spectra from equally abundant peptides, while automatically adjusting to varying abundance ratios of up to 10-to-1. The method was developed for and is demonstrated on peptide spectra, but the authors said that the generality of the methods "allows for their direct application to other types of spectral libraries and mixture spectra."


Journal: Proteomics, March 24 [Epub ahead of print]
Title: HTAPP: high-throughput autonomous proteomic pipeline
Authors: K Yu; AR Salomon

Advances in mass spectrometry, the acceleration of computer processing speeds, and the availability of genomic databases and protein databases has resulted in a "deluge" of proteomic data, making lab-based software for the automated collection, processing, storage, and visualization of expansive proteomic datasets "critically important," according to the authors. Here, they describe HTAPP, "designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample." HTAPP comprises software that controls the acquisition of mass spectral data and the automation of post-acquisition tasks such as peptide quantification, within a "user-configurable lab-based relational database."

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