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Recent Research Papers of Note in Proteomics: Mar 13, 2008

Journal: Nature Methods, March 9 [Epub ahead of print]
Title: Identification of cross-linked peptides from large sequence databases
Authors: O Rinner; J Seebacher; T Walzthoeni; L Mueller; M Beck; A Schmidt; M Mueller; R Aebersold
Described is a method to identify cross-linked peptides from complex samples and large protein sequence databases. Isotopically tagged cross-linkers are combined with chromatographic enrichment, targeted proteomics, and a new search engine called xQuest. The software reduces the search space by an upstream candidate-peptide search before the recombination step. Authors show that xQuest can identify cross-linked peptides from a total E. coli lysate with an unrestricted database search.

Journal: Proteomics, March 7, [Epub ahead of print]
Title: A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen
Authors: JM Asara, HR Christofk; LM Freimark; LC Cantley
Authors demonstrate that a label-free method for relative quantification based on the TIC from peptide MS/MS spectra collected from data-dependent runs can be an effective for quantitative measurements and can expand the dynamic range over isotope labeling experiments allowing for abundance differences up to about 60:1 in a screen for proteins that bind to phosphotyrosine residues.

Journal: Proteomics, March 7 [Epub ahead of print]
Title: Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography
Authors: M Gao; C Deng; W Yu; Y Zhang; P Yang; X Zhang
Authors demonstrate an unbiased method for the large-scale depletion of high-abundance proteins and the identification of middle- or low-abundance proteins by multidimensional LC. The MDLC system, coupling the first dimensional strong cation exchange chromatography with the second dimensional RP-HPLC, was used to deplete high abundance proteins. Sixty-two fractions from strong cation exchange were separated further by RPLC. They observed UV absorption spectra to differentiate high-abundance proteins from middle- and low-abundance proteins. After depleting the high-abundance proteins, the authors enriched, digested, and separated middle- and low-abundance ones by 2D-micro strong cation exchange/cRPLC. Eluted peptides were deposited on the MALDI target and detected by MALDI-TOF/TOF MS.

Journal: Journal of Proteome Research, March 7 [Epub ahead of print]
Title: A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry
Authors: PA DiMaggio; CA Floudas; B Lu; JR Yates
Authors present a novel hybrid method for the automated identification of peptides via de novo integer linear optimization, local database search, and tandem mass spectrometry. They used a modified version of the de novo identification algorithm PILOT to construct accurate de novo peptide sequences and a modified version of the local database search tool FASTA to query these de novo predictions against the non-redundant protein database “to resolve any low-confidence amino acids in the candidate sequences,” according to the abstract.

Journal: Analytical Chemistry, March 6 [Epub ahead of print]
Title: Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting
Authors: EM Woo; D Fenyo; BH Kwok; H Funabiki; BT Chait
Authors describe a “rapid and efficient” method for identifying phosphopeptides. They dub their method mass spectrometric phosphopeptide fingerprinting, which involves quantitative comparison of proteolytic peptides from native versus completely dephosphorylated proteins. In-gel treatment of separated proteins with hydrogen fluoride was done to dephosphorylate serine, threonine, and tryrosine residues, resulting in enrichment of those unmodified peptides that correspond to previously phosphorylated peptides. Quantitative comparison of the signal-to-noise ratios of peaks in the treated versus untreated samples were used to identify phosphopeptides. MS/MS can be used to confirm and further study the phosphopeptides.

Journal: Journal of Mass Spectometry:JMS, March 6 [Epub ahead of print]
Title: Investigations with O-linked protein glycosylations by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry
Authors: TI Williams; DA Saggese; KL Toups; JL Frahm; HJ An; B Li; CB Lebrilla; DC Muddiman
Presented is an examination of sample preparation and MALDI Fourier transform ion cyclotron resonance MS analysis of O-linked glycans globally cleaved from mucin glycoproteins. “Experiments with stable isotope-labeled biomolecules allowed for the establishment of appropriate acquisition times and excitation voltages for MALDI-FT-ICR-MS of oligosaccharides,” according to the abstract, and quadrupole ion guide optimization studies with mucin glycans identified conditions for the analysis of the entire mass range of O-linked carbohydrates in the glycoprotein.

Journal: Accounts of Chemical Research, March 4 [Epub ahead of print]
Title: Subunit architecture of intact protein complexes from mass spectrometry and homology modeling
Authors: T Taverner; H Hernádez, M Sharon; BT Ruotolo; D Matak-Vinkoviæ, D Devos; RB Russell; CV Robinson
Authors are developing a mass spectrometry method based on intact protein complexes to gain more information about interactions between proteins and of their spatial arrangement. They say that by studying intact complexes, the stoichiometry of all subunits present can be determined, and interaction maps and topological arrangements of subunits can be deduced. They construct an interaction network using MS/MS to define peripheral subunits and partial denaturation in solution to generate series of subcomplexes, which are assigned using MS/MS. The authors developed an iterative search algorithm, SUMMIT, to facilitate the assignment process, assigning protein subcomplexes and generating protein interaction networks.

Journal: Journal of Proteome Research, March 4 [Epub ahead of print]
Title: Automatic validation of phosphopeptide identifications by MS2/MS3 Target-Decoy Search Strategy
Authors: X Jiang; G Han; S Feng; X Jiang; M Ye; X Yao; H Zou
A simple automatic validation approach for phosphopeptide identification was developed by combining consecutive stage mass spectrometry data and the target decoy database searching strategy. For further filtering, only phosphopeptides identified by MS2 and MS3 were accepted. Prior to database searching, the spectra were validated for charge state and neutral loss peak intensity. Invalid MS2 and MS3 spectra were removed.

Journal: Journal of Mass Spectrometry, March 4 [Epub ahead of print]
Title: Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry
Authors: S Pourshahian; PA Limbach
According to the abstract, the fractional mass for peptides and oligonucleotides differ due to their different molecular compositions. This has been used to develop the general conditions “necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates.”
Peptides and oligonucleotides created by the theoretical digestion of proteins and nucleic acids were plotted as nominal mass versus factional mass. The plots indicate three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass.
A cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and “conditions for analyzing the sample using … LC-MS were optimized,” authors say in the abstract. Upon analysis of the mixture, detected masses were plotted on a fractional mass plot “and the heteroconjugate could be readily distinguished from non-cross-linked peptides.”

Journal: Rapid Communications in Mass Spectrometry, March 4 [Epub ahead of print]
Title: Serum biomarker profiling by solid-phase extraction with particle-embedded micro tips and matrix-assisted laser desorption/ionization mass spectrometry
Authors: A Navare; M Zhou; J McDonald; FG Noriega; MC Sullards; FM Fernandez
Authors evaluate a new class of solid-phase extraction pipette tips embedded with different chromatographic media for fractionation of model protein digests and serum samples. The embedded materials include strong anion exchange, weak cation exhange, C18, C8, C4, immobilized metal affinity chromatography, and zirconium dioxide particles. The authors describe and test simple and rapid serum proteome profiling protocols based on these SPE micro tips using different MALDI matrices, and show that different types of particle-embedded SPE micro tips give complementary information in terms of spectral features “detected for beta-casein digests and control human serum samples,” according to the abstract.

Journal: Proteomics, March 3 [Epub ahead of print]
Title: Proteomics Data Collection – 2(nd) ProDaC Workshop 5 October 2007, Seoul, Korea
Authors: M Eisenacher; T Hardt; M Hamacher; L Martens; J Häkkinen; F Levander; R Apweiler; HE Meyer; C Stephan
Members of the Proteomics Data Collection, an EU-funded “Coordination Action” within the 6th framework programme, describe their progress. Other representatives presented their experiences and future plans concerning proteomics standards, data handling, and repositories.

Journal: Proteomics, March 3 [Epub ahead of print]
Title: 6(th) HUPO Annual World Congress – Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
Authors: S Orchard; L Martens; J Tasman; PA Binz; JP Albar; H Hermjakob
An update on the current status of PSI is provided. The new MS interchange format, mzML, was entered into the HUPO document process and was “already under active discussion by prospective users,” according to the abstract. It is anticipated to be the de facto standard in 2008.

Journal: Analytical Chemistry, March 1 [Epub ahead of print]
Title: Relative Quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags
Authors: L Dayon; A Hainard; V Licker; N Turck; K Kuhn; DF Hochstrasser; PR Burkhard; JC Sanchez
Authors present and carry out proof-of-principle studies for a new 6-plex isobaric mass tagging technology developed by Proteome Sciences called Tandem Mass Tags. The technology comprises a set of structurally identical tags which label peptides on free amino-terminus and epsilon-terminus functions of lysine residues. Quantification information is obtained during MS/MS fragmentation through the losses of reporter ions.

Journal: Journal of Proteome Research, Feb. 29 [Epub ahead of print]
Title: Development and application of a two-phase, on membrane digestion method in the analysis of membrane proteome
Authors: J Zhou; Y Lin; X Deng; J Shen; Q He; P Chen; X Wang; S Liang
The two-phase system was constituted by mixing n-butanol and 25 micromolars of NH4HCO3. Comparative experiments indicated that proteins on membranes could be digested in the system more efficiently than in both 60 percent methanol and 25 micromolars of NH4HCO3 “thereby improving the identification of the membrane proteins,” according to the abstract. Rat liver membrane proteome was analyzed by the two-phase system and capillary LC-MS/MS, resulting in the identification of 411 membrane proteins of which more than 80 percent were transmembrane proteins with 1 to 12 mapped transmembrane domains.

Journal: Analytical Chemistry, Feb. 29 [Epub ahead of print]
Title: High-throughput nanohole array based system to monitor multiple binding events in real time
Authors: J Ji; JG O’Connell; DJ Carter; DN Larson
Authors developed an integrated label-free, real-time sensing system able to monitor multiple biomolecular biding events. The system is based on changes in the intensity of extraordinary optical transmission through nanohole arrays. The core of the system is a sensing chip with multiple nanohole arrays embedded within an optically thick gold film. Each array, containing 10 by 10 nanoholes, functions as an independent sensor. The integrated system contains a laser light source, a temperature-regulated flow cell encasing the sensing chip, motororized optics, and a charge-coupled detector camera.

Journal: Journal of Proteome Research, Feb. 29 [Epub ahead of print]
Title: Chip-based enrichment and nano-LC-MS/MS analysis of phosphopeptides from whole lysates
Authors: S Mohammed; K Kraiczek; MW Pinkse; S Lemeer; JJ Benschop; AJ Heck
Authors developed a reusable HPLC nanoflow rate chip using TiO2 particles for selective phosphopeptide enrichment. According to the abstract, their chips were robust, easy to use, and performed consistently over tens of analyses “including minute amounts of complex cellular lysates.”

Journal: Bioinformatics, Feb. 28 [Epub ahead of print]
Title: Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline
Authors: AW Dowsey, MJ Dunn; GZ Yang
The method proposed is based on robust automated image normalization, or RAIN, which the authors say circumvents the drawbacks of traditional approaches to high-throughput proteomics. RAIN incorporates a third-order volume invariant B-Spline spline model into a multi-resolution schema “to correct for geometric and expression inhomogeneity at multiple scales,” according to the abstract. The normalized images can be compared directly in the image domain for quantitative differential analysis.

Journal: Journal of Separation Science, Feb. 28 [Epub ahead of print]
Title: A two step fractionation approach for plasma proteomics using immunodepletion of abundant proteins and multi-lectin affinity chromatography: Application to the analysis of obesity, diabetes, and hypertension diseases
Authors: MK Dayarathna; WS Hancock; M Hincapie
A method is proposed utilizing a double fractionation approach combining the MARS immunodepletion column with multi-lectin affinity chromatography to deplete high-abundance proteins in plasma. Authors applied the workflow to a sample set of four groups to determine the suitability of the method: a control pool, and disease pools for obesity, diabetes, and hypertension. According to the abstract, the authors were able to identify changes in the level of several proteins.

Journal: Molecular & Cellular Proteomics, Feb. 25 [Epub ahead of print]
Title: Post-experiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS
Authors: B Shin; HJ Jung; SW Hyung; K Kim; D Lee; C Lee; MH Yu; SW Lee
Authors describe a new method for filtering MS/MS data and refining precursor masses “that provides highly accurate analyses of massive sets of proteomic data,” according to the abstract. The methods, dubbed “post-experiment monoisotopic mass filtering and refinement” comprises a generation of lists of all monoisotopic masses observed in a whole LC-MS experiment; clustering of monoisotopic masses of a peptide into unique mass classes, based on their masses and LC elution times; matching the precursor masses of the MS/MS data to a representative mass of a unique mass class; filtration of the MS/MS data based on the presence of corresponding monoisotopic masses; and refinement of the precursor ions masses by the unique mass class.

Journal: BMC Bioinformatics, Feb. 25 [Epub ahead of print]
Title: Exon level integration of proteomics and microarray data
Authors: DA Bitton; MJ Okoniewski; Y Connolly; CJ Miller
Authors combined quantitative protein mass spectrometry with Affymetrix Exon array data “at the level of individual exons,” according to the abstract, and found significantly higher degrees of correlation between quantitative proteomics and microarray data than had been previously observed.

Journal: Bioinformatics, Feb. 21 [Epub ahead of print]
Title: GOTreePlus: An interactive gene ontology browser for proteomics projects
Authors: B Lee; K Brown; Y Hathout; J Seo
The gene ontology browser developed by the authors, called GOTreePlus, superimposes annotation information over GO structures, and can facilitate the identification of important GO terms “through interactive visualization of them in the GO structure,” according to the abstract.

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