Showing papers in "Molecular & Cellular Proteomics in 2004"

TL;DR: It is found that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression, and the use of 4-fold multiplexing to enable relative protein measurements simultaneously with determination of absolute levels of a target protein using synthetic isobaric peptide standards.

TL;DR: This work uses the sub-parts per million mass accuracy of a new ion trap Fourier transform mass spectrometer to achieve more than a 100-fold increased confidence in peptide identification compared with typical ion trap experiments and shows that trypsin cleaves solely C-terminal to arginine and lysine.

TL;DR: Most major categories of proteins in the human proteome are represented in plasma, with the distribution at successively deeper layers shifting from mostly extracellular to a distribution more like the whole (primarily cellular) proteome.

TL;DR: Although the overall pattern of protein expression is similar to that of mRNA expression, the incongruent expression between mRNAs and proteins emphasize the importance of posttranscriptional regulatory mechanisms in cellular development or perturbation that can be unveiled only through integrated analyses of both proteins and m RNAs.

TL;DR: This review focuses more on questions that cast doubt on the results reported and proposes experiments to investigate these questions in detail, before the technique is used at the clinic.

TL;DR: In an effort to ensure that high-quality, significant data are entering the proteomics literature, Molecular & Cellular Proteomics (MCP) is introducing guidelines for authors planning to submit manuscripts containing large numbers of proteins identified primarily by LC-MS/MS.

TL;DR: Ovarian cancer is characterized by few early symptoms, presentation at an advanced stage, and poor survival, and it is the most frequent cause of death from gynecological cancer as discussed by the authors.

TL;DR: This work reports the use of a mass spectrometry-based methodology permitting the first proteomic-scale phosphorylation site analysis of primary animal tissue, identifying over 500 proteinosphorylation sites in the developing mouse brain.

TL;DR: A proteomics method for determining the subcellular localization of membrane proteins in both the endoplasmic reticulum and the Golgi apparatus in Arabidopsis using a new tool for high-throughput protein localization by isotope tagging.

TL;DR: This approach provided for the first time a snapshot of the protein components of the TIF, which shows consists of more than one thousand proteins—either secreted, shed by membrane vesicles, or externalized due to cell death—produced by the complex network of cell types that make up the tumor microenvironment.

TL;DR: A review of 80 published studies encompassing more than 25,000 patients designed to consider the relative advantages and disadvantages of the various methods of measuring HER-2/neu in clinical breast cancer specimens is presented in this paper.

TL;DR: Proteomic analysis confirmed the expression of many previously unreported genes in platelets, and identified 82 proteins secreted from activated platelets and compared these, as well as published proteomic data, to the transcriptional profile.

TL;DR: DHA is a more potent RXR ligand than previously observed, inducing robust RXR activation already at low micromolar concentrations, and it is shown that other naturally occurring PUFAs can activate RXR with similar efficiency as DHA, suggesting that RXR could function as a fatty acid receptor in vivo.

TL;DR: The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests, and can be used for accurate prediction of retention times fortryptic peptide on reversed-phase columns of different sizes with a linear water-ACN gradient and with TFA as the ion-pairing modifier.

TL;DR: The identification of 452 proteins isolated from biochemically purified PSD fractions of rat and mouse brains using nanoflow HPLC coupled to electrospray tandem mass spectrometry suggests new mechanisms by which the PSD helps regulate synaptic strength and transmission.

TL;DR: A new proteomic strategy based on mass spectrometry analyses of a plasma membrane fraction enriched in hydrophobic proteins is developed, showing a correlation between the putative functions of the identified proteins and the expected roles for plasma membrane in transport, signaling, cellular traffic, and metabolism.

TL;DR: This report compared the expression levels for more than 440 proteins in the microsomal fractions of prostate cancer cells with varying metastatic potential and found 60 were found elevated greater than 3-fold in the highly metastatic cells, whereas 22 were reduced by equivalent amounts.

TL;DR: The study demonstrates significant post-transcriptional control of protein levels for a number of different compartments and functional modules, which is missed when exclusively focusing on transcript levels.

TL;DR: The paper that follows attempts to highlight the strengths and weaknesses of the methods in current use, as well as establishing criteria for mass spectrometric identification of proteins that should be employed by researchers.

TL;DR: This work explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone and found that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions.

TL;DR: An analysis of the red blood cell proteome by ion trap tandem mass spectrometry in line with liquid chromatography found 181 unique protein sequences, including membrane skeletal proteins, metabolic enzymes, transporters and channel proteins, adhesion proteins, hemoglobins, cellular defense proteins, proteins of the ubiquitin-proteasome system, and others.

TL;DR: In this article, an integrated suite of algorithms, statistical methods, and computer applications is developed to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures.

TL;DR: Serum CK19 level might reflect the pathological progression in some HCC and may be a useful marker for predicting tumor metastasis and a therapeutic target for the treatment of HCC patients with metastases.

TL;DR: In this paper, the authors present a review of all three developmental phases including the repertoire of discovery tools for protein separation as well as giving an outline of modern principles of mass spectrometry for the identification of proteins.

TL;DR: The results show that the clinical proteomic method using LCM coupled with ICAT and 2D-LC-MS/MS can carry out not only large-scale but also accurate qualitative and quantitative analysis.

TL;DR: Analysis of the proteome of Mycobacterium tuberculosis reveals that different proteomic technologies applied to the same sample provide complementary types of information that contribute to a more complete understanding of the biological system studied.

TL;DR: It is shown that dialysis permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE, and protein complexes of various proteins including the tumor suppressor p53 and c-Myc are identified via mass spectrometry showing that the method has a wide potential for functional proteomics.

TL;DR: It is shown here that MudPIT reproducibly identified bona fide partners for budding yeast Gcn5p and that it is feasible for an investigator working with a single ion trap instrument in a conventional molecular/cellular biology laboratory to carry out proteomic characterization of a pathway, organelle, or process by systematic application of TAP-MudPIT.

TL;DR: The strategy described in this study should be generally applicable for a detailed proteomic analysis of most body fluids and in combination with “tagging” approaches for differential proteomics could be used for identification of cancer biomarkers from any body fluid.

TL;DR: Immunochemical methods confirmed that anterior gradient-2 is universally up-regulated in Barrett’s epithelium, relative to normal squamous tissue derived from the same patient, identified as a novel survival factor whose study may shed light on cellular pathways that attenuate the tumor suppressor p53.