Journal ArticleDOI
Quantitative proteomic analysis by accurate mass retention time pairs.
Jeffrey C. Silva,Richard Denny,Craig A. Dorschel,Marc V. Gorenstein,Ignatius J. Kass,Guo-Zhong Li,Therese McKenna,Michael J. Nold,Keith Richardson,Phillip Young,Scott J. Geromanos +10 more
TLDR
The principal focus of this paper will demonstrate the quantitative aspects of the methodology and continue with a discussion of the associated, complementary qualitative capabilities.Abstract:
Current methodologies for protein quantitation include 2-dimensional gel electrophoresis techniques, metabolic labeling, and stable isotope labeling methods to name only a few. The current literature illustrates both pros and cons for each of the previously mentioned methodologies. Keeping with the teachings of William of Ockham, “with all things being equal the simplest solution tends to be correct”, a simple LC/MS based methodology is presented that allows relative changes in abundance of proteins in highly complex mixtures to be determined. Utilizing a reproducible chromatographic separations system along with the high mass resolution and mass accuracy of an orthogonal time-of-flight mass spectrometer, the quantitative comparison of tens of thousands of ions emanating from identically prepared control and experimental samples can be made. Using this configuration, we can determine the change in relative abundance of a small number of ions between the two conditions solely by accurate mass and retention...read more
Citations
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Andromeda: a peptide search engine integrated into the MaxQuant environment
Jürgen Cox,Nadin Neuhauser,Annette Michalski,Richard A. Scheltema,Jesper V. Olsen,Matthias Mann +5 more
TL;DR: A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.
Journal ArticleDOI
Quantitative mass spectrometry in proteomics: a critical review
TL;DR: This review critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discusses challenges in arriving at meaningful interpretations of quantitative proteomic data.
Journal ArticleDOI
Absolute Quantification of Proteins by LCMSE A Virtue of Parallel ms Acquisition
TL;DR: A new method of absolute quantification of proteins is described, based on the discovery of an unexpected relationship between MS signal response and protein concentration, which is constant within a coefficient of variation of less than ±10%.
Journal ArticleDOI
Protein Analysis by Shotgun/Bottom-up Proteomics
TL;DR: The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis.
Journal ArticleDOI
Orthogonality of separation in two-dimensional liquid chromatography.
TL;DR: The RP-RP system (employing significantly different pH in both RP separation dimensions) had the highest practical peak capacity of 2D-LC systems investigated and was found to provide suitable orthogonality.
References
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Journal ArticleDOI
Maximum entropy image reconstruction: general algorithm
John Skilling,R. K. Bryan +1 more
TL;DR: Le maximum d'entropie (LDE) as mentioned in this paper is a technique optimale de reconstruction d'image, largement applicable en astronomie, and it is capable of generer des images provenant d'une large variete de types de donnees.
Journal ArticleDOI
Matrix effect in quantitative LC/MS/MS analyses of biological fluids: a method for determination of finasteride in human plasma at picogram per milliliter concentrations.
TL;DR: Development of a highly sensitive assay for I in human plasma at low picogram per milliliter concentrations using LC/MS/MS with a heated nebulizer (HN) interface, instead of a TISP interface, is described, practically eliminating the ion suppression.
Journal ArticleDOI
Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics
Jeroen Krijgsveld,René F. Ketting,Tokameh Mahmoudi,Tokameh Mahmoudi,Janik Johansen,Marta Artal-Sanz,C. Peter Verrijzer,C. Peter Verrijzer,Ronald H.A. Plasterk,Albert J. R. Heck +9 more
TL;DR: In this article, the authors describe quantitative 15N metabolic labeling of the multicellular organisms Caenorhabditis elegans, a nematode and Drosophila melanogaster, the common fruit fly, achieved by feeding them on 15N-labeled Escherichia coli and yeast, respectively.
Journal ArticleDOI
18O labeling: a tool for proteomics.
TL;DR: The evaluation of the relative Ziptip efficiency indicated a loss in sample recovery as the peptide concentration was reduced using normal conditions, suggesting that there is a limit below which there are diminishing returns.
Journal ArticleDOI
Ion suppression effects in liquid chromatography-electrospray-ionisation transport-region collision induced dissociation mass spectrometry with different serum extraction methods for systematic toxicological analysis with mass spectra libraries.
TL;DR: It could be demonstrated, that ion suppression is not generally present at any retention time when using reversed-phase HPLC with rather long gradient programs, but may play an important role in case of high-throughput LC-MS analysis, when the analyte is not separated from the LC-front, or in flow injection analysis without chromatographic separation.