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Recent Research Papers of Note: Jun 25, 2009


Journal: Rapid Communications in Mass Spectrometry: RCM, July
Title: Fragmentation behavior of metal-coded affinity tag (MeCAT)-labeled peptides
Authors: S Pieper; S Beck; R Ahrends; C Scheler; MW Linscheid

According to the authors, MeCAT can be used for both relative and absolute quantification, and for structural information, knowledge about the fragmentation behavior of MeCAT-modified peptides is "highly beneficial." They studied the fragmentation behavior of MeCAT-labeled peptides under collision induced dissociation, electron capture dissociation, and infrared multiphoton dissociation conditions. Application of CID and ECD "allowed a straightforward sequence elucidation of MeCAT-labeled peptides," they said. During IRMPD, all MeCAT-labeled peptides formed characteristic fragments "resulting from the fragmentational cleavage of the tagging group, thus providing a screening method for the identification of labeled compounds," the authors said.

Journal: Bioinformatics, June 15
Title: Proteome coverage prediction with infinite Markov models
Authors: M Claasen; R Aebersold; JM Buhmann

LC-MS/MS is the predominant method for comprehensive characterization of complex protein mixtures, according to the abstract, and to maximize proteome coverage of a studied sample, LC-MS/MS experiments are typically repeated and the results combined. Proteome coverage prediction is necessary to improve the design of efficient proteomics studies, but there is no method to "reliably estimate the increase of proteome coverage at an early stage." In their study, the authors propose an extended infinite Markov model DiriSim "to extrapolate the progression of proteome coverage based on a small number of already performed LC-MS/MS experiments," according to the abstract. The method, they said, "explicitly accounts for the uncertainty of peptide identifications."

Journal: Molecular & Cellular Proteomics, June 13 [Epub ahead of print]
Title: An integrated approach for differential mass spectrometry and gene ontology analysis identified novel proteins regulating neuronal differentiation and survival
Authors: K Kobayashi J Kumagai; T Morikawa; M Wilson-Morifuji; A Wilson; A Irie; N Araki

Authors used iTRAQ-based quantitative differential LC-MS/MS, functional annotation with a proprietary gene ontology tool, Molecular ANnotation by Gene Ontology, or MANGO, and standard biochemical methods to identify proteins related to neuronal differentiation in nerve-growth factor-treated rat pheochromocytoma cells. Nano-LC-MALDI-MS/MS and nano-LC-ESI-MS/MS were performed for maximum proteome coverage.

Journal: Analytical Chemistry, June 12 [Epub ahead of print]
Title: Comprehensive and reliable phosphorylation site mapping of individual phosphoproteins by combination of multiple stage mass spectrometric analysis with a target-decoy database search
Authors: G Han; M Ye; X Jiang; R Chen: J Ren; Y Xue; F Wang; C Song; X Yao; H Zou

Presented is a modified target-decoy database search strategy for phosphorylation-site analysis of individual phosphoproteins without manual interpretation of data. A composite database constructed for analysis included only the sequences of the individual target proteins and a decoy version of a small inhomogeneous protein database, rather than a target-decoy database that used all protein sequences in a proteome database of an organism. The confidence of phosphopeptide identification could be controlled when the acquired MS2 and MS3 spectra were searched against the constructed composite database followed by data processing.

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Journal: Journal of Proteome Research, June 8 [Epub ahead of print]
Title: Multiple products monitoring as a robust approach for peptide quantification
Authors: JH Baek; H Kim; B Shin; MH Yu
According to the authors, quantification approaches such as selected reaction monitoring and multiple reaction monitoring aren't widespread because they are so time-consuming. In the study, they describe an approach for quantifying target peptides "without such an arduous process of ion selection." The method is based on monitoring multiple product ions from full-range MS2 spectra of a target precursor. Their method uses a scoring system "that considers both the absolute intensities of product ions and the similarities between the query MS2 spectrum and the reference MS2 spectrum of the target peptide," according to the abstract. "Compared with conventional approaches, MpM greatly improves sensitivity and selectivity of peptide quantification using an ion-trap mass spectrometer," the authors said.

Journal: Journal of Proteome Research, June 8 [Epub ahead of print]
Title: Enhanced sensitivity in proteomics experiments using FAIMS coupled with a hybrid linear ion trap/Orbitrap mass spectrometer (dagger)
Authors: J Saba; E Bonneil; C Pomiès; K Eng; P Thibault

Described is the use and application of high-field asymmetric waveform ion mobility spectrometry combined with nanoscale LC-MS to improve the sensitivity and dynamic range of proteomics analysis on a hybrid LTQ-Orbitrap.

Journal: Journal of Proteome Research, June 8 [Epub ahead of print]
Title: A comparison of labeling and label-free mass spectrometry-based proteomics approaches
Authors: VJ Patel; K Thalassinos; SE Slade; JB Connolly; A Crombie; JC Murrell; JH Scrivens

Three profiling and comparative approaches were used to characterize the proteome of the recently discovered bacterium Methylocella silvestris. The organism was grown on two different substrates "enabling variations in proteins expression to be identified," and results obtained with the different approaches were compared in terms of the number of proteins identified, confidence in identification, sequence coverage, and agreement of regulated proteins.

Journal: Methods of Information in Medicine, June 5
Title: Geometric alignment of 2D gel electrophoresis images
Authors: S Wörz; ML Winz; K Rohr

Proposed is a method of accurate geometric alignment of 2DE images in order to cope with variations in locations of proteins in the different images. A new elastic registration approach for such images is introduced, which is based on an analytic solution of the Navier equation using Gaussian elastic body splines. Cross effects in elastic deformation can be handled, and landmark correspondences can included "to aid the registration in regions which are difficult to register using intensity information alone," according to the abstract.

Journal: Proteomics, June 5 [Epub ahead of print]
Title: A comparison of MS/MS-based, stable-isotope-labeled, quantitation performance on ESI-quadrupole TOF and MALDI-TOF/TOF mass spectrometers
Authors: MA Kuzyk; LB Ohlund; MH Elliott; D Smith; H Qian; A Delaney; CL Hunter; CH Borchers

Based on the comparison of the two platforms, the authors conclude that overall MS/MS based peptide quantitation performance of the offline LC-MALDI was comparable with online LC-ESI, which required three-fold less time. Offline LC-MALDI allows for archived HPLC-separated samples to be reanalyzed, however.

Journal: Journal of Proteome Research, June 4 [Epub ahead of print]
Title: Protein profile of capacitated versus ejaculated human sperm
Authors: F Secciani; L Bianchi; L Ermini; R Ciani; A Armini; GG La Scala; R Focarelli; L Bini; F Rosati

"Freshly ejaculated sperm acquire the fertilizing potential by a continuing process that occurs during sperm transport through the female genital tract, and it is physiologically not complete until the spermatozoon reaches the oocyte," according to the abstract. This process called capacitation can be mimicked in vitro by use of appropriate capacitation media, but the molecular mechanisms of capacitation are "poorly understand." The study describes a proteomic analysis of "protein profile variations in human normospermic samples as a consequence of three hours in vitro capacitation," the authors said.

Journal: Journal of Proteome Research, June 3 [Epub ahead of print]
Title: Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach
Authors: N Pfeifer; A Leinenbach; CG Huber; O Kohlbacher

Described is a method to model of 2D peptide separation based on reversed-phase and ion-pair reversed phase HPLC combined with a computation method to model and predict retention times in both dimensions. The algorithm uses statistical learning "to establish a retention model from about 200 peptide retention times and their corresponding sequences," according to the abstract. Application of retention-time prediction to the peptides leads to improvements in true positive peptide identifications upon lowering mass spectrometric scoring thresholds "and concomitantly filtering out false positives on the basis of predicted retention times," the authors said. The method increased peptide identifications by about 19 percent at a q value of .01 in a whole proteome measurement, the authors said.

Journal: Journal of Proteome Research, June
Title: Expediting the development of targeted SRM assay: Using data from shotgun proteomics to automate method development
Authors: A Prakash; DM Tomazela; B Frewen; B Maclean; G Merrihew; S Peterman; MJ MacCoss

While SRM is a powerful MS/MS method for monitoring target peptides within a complex protein digest, "an underappreciated step in the development of an assay to measure many peptides in parallel is the time and effort necessary to establish a useable assay," according to the abstract. The authors report the use of shotgun proteomics data to hasten the selection of SRM transitions for target peptides of interest. They also present a scoring routine that can be used to compare the targeted SRM chromatogram data with an MS/MS spectrum acquired by data-dependent acquisition and stored in a library.

Journal: Journal of Agricultural and Food Chemistry, June
Title: Functional proteomic analysis predicts beef tenderness and tenderness differential
Authors: I Zapata; HN Zerby; M Wick

In an effort to understand the mechanisms behind inconsistent meat tenderness, authors performed functional proteomics to associate electrophoretic bands from the myofibrillar muscle fraction to meat tenderness. The myofibrillar muscle fraction of the Longissimus dorsi from 22 Angus cross steers were analyzed by SDS-PAGE and "linearly regressed to Warner-Bratzler shear values," according to the abstract. Six significant electrophoretic bands were characterized and sequenced. "The proteins/peptides identified in these bands encompass a wide array of cellular pathways related to structural, metabolic, chaperone, and developmental functions," according to the abstract. The study, the authors added, begins to assemble information that had been previously reported "into a more complete picture that will lead to the establishment of a coherent mechanism accounting for meat tenderness."

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Journal: Proteomics, June
Title: Confidence assessment for protein identification by using peptide-mass fingerprinting data
Authors: Z Song; L Chen; D Xu

According to the authors, Peptide Mass Fingerprinting, while an important method of protein identification, still has problems, including false positive identification due to current computational methods and identification scores that are not normalized when assigned singly by a scoring function. To address the latter, they developed a statistical model for the evaluation of the confidence of a raw score and improve the rankings of proteins for identification. Their study, they said, describes a new method for enhancing protein identification accuracy by using PMF data.

Journal: Proteomics, June
Title: Multiplexed LC-MS/MS analysis of horse plasma proteins to study doping in sport
Authors: C Barton; P Beck; R Kay; P Teale; J Roberts

"The development of protein biomarkers for the indirect detection of doping in horse is a potential solution to doping threats such as gene and protein doping," according to the abstract. Presented is a method of biomarker discovery in horse plasma using targeted analysis of proteotypic peptides in horse proteins. The method is optimized and validated and then applied to a group of race horses to study protein variation within a population.

Journal: Proteomics, June
Title: A sensitive magnetic bead method for the detection and identification of tyrosine phosphorylation in proteins by MALDI-TOF/TOF MS
Authors: MR Condina; MA Guthridge; SR McColl; P Hoffmann

Phosphorylation occurs in an estimated 30 percent of the mammalian proteome and is implicated in many diseases, according to the abstract, yet current proteomic approaches for the assessment of tyrosine phosphorylation are inadequate. The authors describe a reproducible, high-sensitivity method for detecting and mapping phosphotyrosine residues by mass spectrometry that couples the anti-phosphotyrosine antibody 4G10 covalently to super para-magnetic beads or by affinity to super para-magnetic beads with protein G covalently attached. The approach, the authors said, allowed them to enrich phosphotyrosine peptides mixed with non-phosphorylated peptides at a ratio of 1:200, "enabling detection at a level representing the highest sensitivity reported for tyrosine phosphorylation," according to the abstract. The beads were then used to enrich tyrosine phosphopeptides from a digest of the in vitro-phosphorylated recombinant beta-intracellular region of the granulocyte-macrophage colony-stimulating factor receptor. This was subsequently analyzed by MALDI-TOF/TOF MS.

Journal: Journal of Chromatography. B, Analytical technologies in the biomedical and life sciences, May 29 [Epub ahead of print]
Title: A new strategy for protein biomarker discovery utilizing 2-nitrobenzenesulfenyl (NBS) reagent and its applications to clinical samples
Authors: EI Matsuo; M Watanabe; H Kuyama; O Nishimura

Authors have refined a method they developed earlier using both tryptophan-targeted stable isotope tagging and mass spectrometry for the quantitative analysis of a proteome. They now replace detergents and an enrichment column and further use a novel matrix suitable for tagged peptides. They constructed a total analytical system combining the new method with HPLC, an automatic spotter, MALDI-TOF MS, and analytical software and applied it to clinical samples such as colorectal carcinoma and renal cell carcinoma.

Journal: Molecular & Cellular Proteomics, May 24 [Epub ahead of print]
Title: Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis.
Authors: RW Sprung; JW Brock; JP Tanksley; M Li; MK Washington; RJ Slebos; DC Liebler
Formalin-fixed paraffin-embedded tissue specimens are a potentially valuable resource for retrospective biomarker discovery studies and recent studies suggest the feasibility of using shotgun proteomics for the characterization of FFPE tissue proteins, the authors said in the abstract. Here, they compare shotgun proteomic analysis of frozen and FFPE specimens prepared from the same colon adenoma tissues. Their data "demonstrate the equivalence of proteome inventories obtained from FFPE and frozen tissue specimens and provide support for retrospective proteomic analysis of FFPE tissues for biomarker discovery," according to the abstract.

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