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Recent Research Papers of Note in Proteomics: Feb 22, 2007

Journal: Brain Research, Feb. 23
Title: Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: Mapping of neurotransmitter receptors and ion channels
Authors: JV Olsen; PA Nielsen; JR Andersen; M Mann; JR Wisniewski
Authors used recently developed methods for isolation of membrane proteins from 10-20 milligram brain tissue to perform a proteomic quantitative analysis of three distinct compartments of the mouse brain — cortex, hippocampus, and cerebellum. Authors quantified 976 unique peptides corresponding to 555 unique proteins and report that up to two-fold differences in the levels of some proteins between brain areas were measured.
“Our results clearly demonstrate differences in levels of membrane proteins mapped in distinct brain compartments and offer a technology that allows in depth study of brain membrane proteomes, such as mouse models of neurological diseases,” the authors say in the study’s abstract.

Journal: Proteomics, Feb. 19 [Epub ahead of print]
Title: Infrared-based protein detection arrays for quantitative proteomics
Authors: C Loebke; H Sueltmann; C Schmidt; F Henjes; S Wiemann; A Poustka; U Korf
Authors present a protein microarray-based approach toward the sensitive detection of proteins in the fentogram range, based on signal detection in the near-infrared range. Protein abundance is determined qualitatively, and quantitatively, if recombinant protein is available.

Journal: Analytical Chemistry, Feb. 17 [Epub ahead of print]
Title: Multiplexed ion mobility spectrometry-orthogonal time-of-flight mass spectrometry
Authors: ME Belov; MA Buschbach; DC Prior; K Tang; RD Smith
Authors developed a multiplexed ESI-IM-TOF MS that enables lossless ion transmission through the IMS-TOF and a utilization efficiency of greater-than 50 percent for ions from the ESI source.
“Initial results with a mixture of peptides show a approximately 10-fold increase in signal-to-noise ratio with the multiplexed approach compared to a signal averaging approach, with no reduction in either IMS or TOF MS resolution,” the authors say in the abstract.

Journal: Journal of the American Society for Mass Spectrometry, Feb. 15 [Epub ahead of print]
Title: Free radical-induced site-specific peptide cleavage in the gas phase: Low-energy collision-induced dissociation in ESI- and MALDI mass spectrometry
Authors: H Yin; A Chacon; NA Porter; H Yin; DS Masterson
Authors report that amino groups of lysine residue in peptides can be selectively modified by reaction with a peroxycarbonate and the resulting lysine peroxycarbamates can undergo hemolytic fragmentation under conditions of low-energy CID in ESI and MALDI MS. The ensuing selective modification of lysine residue in peptides can induce specific peptide cleavage at or near the lysine site, the authors say in the abstract. Such strategies could aid in protein sequencing analysis and have potential applications in top-down proteomics, the authors say.

Journal: The FEBS Journal, February 2007
Title: Proteomics of Yynechocystis sp. PCC 6803
Author: T Pisareve; M Shumskaya; G Maddalo; L Ilag; B Norling
Authors set out to identify integral membrane proteins found in the cyanobacterial plasma membrane. Authors enriched integral proteins from purified plasma membranes of Synechocystis sp. PCC 6803 by using urea, followed by protein resolution in 1D SDS/PAGE. They found 51 proteins by peptide mass fingerprinting using MALDI-TOF MS.

Journal: Annual Review of Biophysics and Biomolecular Structure, Feb. 8 [Epub ahead of print]
Title: Single-molecule fluoroscence analysis of cellular nanomachinery components
Author: R Peters
The author set out to examine whether single-molecule fluorescence analysis can analyze individual protein complexes in living cells and tissues at high speed. He says that while SMF methods provide “powerful, indispensable tools for the structural and functionally characterization of protein complexes…the transition from in vitro to living cells is in the initial stages.”

Journal: Journal of Proteome Research, Feb. 8, [Epub ahead of print]
Title: Development of reagents for differential protein quantitation by subtractive parent (precursor) ion scanning
Authors: A Wahlander; G Arrigoni; K Warell; F Levander; R Palmgren; JL Maloisel; P Busson; P James
Authors describe a method for quantitative differential proteomics that reduces data complexity in proteome analysis by automated selection of peptides for MS/MS analysis according to their isotope-labeling ratio. They developed isotopic reagents giving products that fragment easily, generating a unique pair of signature ions. By using the ion-pair ratio, they show that it is possible to select only BSA peptides for MS/MS when spiked in a whole yeast extract using parent (precursor) ion quantitation scanning (PIQS) for MS/MS.

Journal: Bioinformatics, Feb. 3, [Epub ahead of print]
Title: Hardware acceleration of processing of mass spectrometric data for proteomics
Authors: I Bogdan; D Coca; J Rivers; RJ Beynon
Authors describe a strategy allowing for real-time advance processing of mass spectrometric data, making use of the reconfigurable computing paradigm. They describe a reconfigurable computing solution for processing raw data generated by MALDI-TOF MS.

Journal: Proteome Science, Feb. 1 [Epub ahead of print]
Title: An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ
Authors:JA Siepen; N Swainston; AR Jones; SR Hart; H Hermjakob; P Jones; SJ Hubbard
Authors propose an extension to the PRIDE and mzData XML schema “to accommodate the concept of multiple samples per experiment” and to capture the intensities of the iTRAQ reporter ions in the entry.

Journal: Journal of Proteome Research, Feb. 6
Title: A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes
Authors: K Kito; K Ota; T Fujita; T Ito
Authors describe a novel peptide-concatenated standard strategy for accurate MS quantification of component stoichiometry of multiprotein complexes. Peptides suitable for quantification are selected with their natural flanking sequences from each component of the multiprotein complexes and concatenated into a single synthetic protein.

Journal: Journal of Proteome Research, Feb. 2
Title: An iTRAQ-based quantitative analysis to elaborate the proteomic response of Nostoc sp.PCC 7120 under N(2) fixing conditions
Authors: K Stensio; SY Ow; ME Barrios-Llerena; P Lindblad; PC Wright
Authors characterized and quantified the proteome of the Nostock sp. PCC 7120 wild-type strain grown under N2 fixing and non-N2 fixing conditions. Measurements were then made using iTRAQ on a whole cell digest to assess global proteome changes in response to environmental changes. Authors say they identified 486 proteins across two biological replicate experiments where 226 experiments contained two or more distinct peptides.

Journal: Analytical Chemistry, Feb. 1
Title: Relative information content and top-down proteomics by mass spectrometry: utility of ion/ion proton-transfer reactions in electrospray-based approaches
Authors: J. Liu; PA Chrisman; DE Erickson; SA McLuckey
Authors examined the informing power associated with “top-down” proteomics implemented with commonly used mass analyzers, such as quadrupole ion trap and time-of-flight mass spectrometers, by using a computer to simulate electrospray ionization and collision-induced dissociation experiments.

Journal: Rapid Communications in Mass Spectrometry: RCM, Feb. 6
Title:Structural analysis of O-glycopeptides employing negative- and positive-ion multi-stage mass spectra obtained by collision-induced and electron-capture dissociations in linear ion trap time-of-flight mass spectrometry
Authors: K Deguchi; H Ito; T Baba; A Hirabayashi; H Nakagawa; M Fumoto; H Hinou; SI Nishimura
Authors describe an MS-based approach combining collision-induced dissociation and electron capture dissociation in the positive-and negative-ion modes as a simple and direct method of assigning an O-glycan without releasing it from the peptide and determining the amino acid sequence of the peptide and glycosylation site.

Journal: Methods in Molecular Biology, 2007
Title: A rapid, economical, and reproducible method for human serum delipidation and albumin IgG removal for proteomic analysis
Authors: Q Fu; DE Bovenkamp; JE Van Eyk
In order to facilitate the identification of disease biomarkers in human serum, authors describe a method of removing albumin and immunoglobulin from serum involving delipidation from centrifugation, IgG removal with protein G Sepharose, and HSA depletion with sodium chloride/ethanol precipitation. The protocol is streamlined to increase reproducibility.

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