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Michael Bartlet-Jones

Other affiliations: Lincoln's Inn
Bio: Michael Bartlet-Jones is an academic researcher from Life Technologies. The author has contributed to research in topics: Analyte & Multiplex. The author has an hindex of 8, co-authored 17 publications receiving 4762 citations. Previous affiliations of Michael Bartlet-Jones include Lincoln's Inn.

Papers
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Journal ArticleDOI
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.

4,411 citations

Journal ArticleDOI
15 Sep 2000-Cell
TL;DR: Purified IP6 is bound by DNA-PK and specifically stimulates DNA- PK-dependent end-joining in vitro, which is of particular interest since the catalytic domain ofDNA-PKcs is similar to that found in the phosphatidylinositol 3 (PI 3)-kinase family.

254 citations

Journal ArticleDOI
TL;DR: A conceptually novel approach to protein sequencing involves the generation of ragged-end polypeptide chains followed by mass spectroscopic analysis of the resulting nested set of fragments that allows the identification of several consecutive residues starting with a few picomoles of peptide.
Abstract: A conceptually novel approach to protein sequencing involves the generation of ragged-end polypeptide chains followed by mass spectroscopic analysis of the resulting nested set of fragments. We report here on the synthesis and development of a volatile isothiocyanate (trifluoroethylisothiocyanate) that allows the identification of several consecutive residues starting with a few picomoles of peptide. The nested set of peptides is generated simply by adding equal aliquots of starting peptide each cycle and driving both the coupling and cleavage reactions to completion. No additional reagents are required to act as chain terminators and retention of the peptide terminal amine allows for subsequent modification with quaternary ammonium alkyl NHS esters to improve sensitivity. Complex washing procedures are not required each cycle, as reagents and by-products are efficiently removed under vacuum, eliminating extractive loss. Multiple peptide samples can be processed simultaneously, with each degradation cycle completed in 35-40 min. The inherent simplicity of the process should allow for easy automation and permit rapid processing of samples in parallel.

99 citations

Journal ArticleDOI
TL;DR: Derivatization procedures for peptides are described that can be performed with sub-picomolar amounts of sample and that are able to direct the formation of fragment ions in Postsource Decay (PSD) MALDI mass spectrometry, which appears to be favorably applicable to sequence analysis of unknown peptides.

68 citations

Book ChapterDOI
01 Jan 1996
TL;DR: The sheer number of proteins is too great to permit large-scale characterization within any useful period of time, and the use of monoclonal antibodies, whilst both rapid and extremely sensitive, requires the ready availability of a large pool of antibody probes.
Abstract: Large-format 2D gel electrophoresis systems have been developed that are capable of resolving several thousand cellular proteins in a matter of days [1,2]. For a number of years, a combination of Edman microsequence analysis and identification of proteins by staining with specific antibodies has been used to systematically categorize proteins and establish cellular databases [3, 4, 5]. There are, however, significant problems associated with these approaches. Most resolved proteins are only present in the low- to upper-femtomole range, significantly below the level at which automated sequencers can reliably operate [6, 7]. The relatively slow speed of the Edman process (one or two samples per machine per day) also means that the sheer number of proteins is too great to permit large-scale characterization within any useful period of time. The use of monoclonal antibodies, whilst both rapid and extremely sensitive, requires the ready availability of a large pool of antibody probes.

38 citations


Cited by
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Journal ArticleDOI
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
Abstract: Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.

8,195 citations

Journal ArticleDOI
TL;DR: A new intensity determination and normalization procedure called MaxLFQ is developed that is fully compatible with any peptide or protein separation prior to LC-MS analysis, which accurately detects the mixing ratio over the entire protein expression range, with greater precision for abundant proteins.

3,732 citations

Journal ArticleDOI
TL;DR: Current understanding of the major factors regulating protein expression is summarized to demonstrate a substantial role for regulatory processes occurring after mRNA is made in controlling steady-state protein abundances.
Abstract: Recent advances in next-generation DNA sequencing and proteomics provide an unprecedented ability to survey mRNA and protein abundances. Such proteome-wide surveys are illuminating the extent to which different aspects of gene expression help to regulate cellular protein abundances. Current data demonstrate a substantial role for regulatory processes occurring after mRNA is made - that is, post-transcriptional, translational and protein degradation regulation - in controlling steady-state protein abundances. Intriguing observations are also emerging in relation to cells following perturbation, single-cell studies and the apparent evolutionary conservation of protein and mRNA abundances. Here, we summarize current understanding of the major factors regulating protein expression.

3,308 citations

Journal ArticleDOI
TL;DR: An updated protocol covering the most important basic computational workflows for mass-spectrometry-based proteomics data analysis, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques is presented.
Abstract: MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda This protocol update describes an adaptation of an existing protocol that substantially modifies the technique Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs) The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores The software is written in C# and is freely available at http://wwwmaxquantorg

2,811 citations

Journal ArticleDOI
21 Apr 2016-Cell
TL;DR: It is concluded that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.

1,996 citations