Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

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.

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Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

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

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

On the Dependency of Cellular Protein Levels on mRNA Abundance.

Mass spectrometry is a central analytical technique for protein research and for the study of biomolecules in general. Driven by the need to identify, characterize, and quantify proteins at ever increasing sensitivity and in ever more complex samples, a wide range of new mass spectrometry-based analytical platforms and experimental strategies have emerged. Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science.

https://science.sciencemag.org/content/sci/312/5771/212.full.pdf

Mass spectrometry and protein analysis.

Methods, compositions and libraries pertaining pna dimer and pna oligomer synthesis

A composition, method, and kit for calibrating a mass spectrometer including a predetermined concentration of a calibrant having a mixture of amino acid polyethylene glycol compounds and a solvent for dissolving the calibrant. The calibrant can be used in either positive or negative ionization mode, and it can be used in calibrating an atmospheric pressure chemical ionization or an electrospray mass spectrometer. The calibrant can include a mixture to enable calibration across a broad range of masses.

Composition, method, and kit for calibrating a mass spectrometer

This invention pertains to methods, mixtures, kits and compositions pertaining to analyte determination and/or quantification by mass spectrometry using compounds comprising a reporter moiety and a non-encoded detectable label. The compounds can be used in sets for the analysis of mixtures of labeled analytes.

Analyte determination utilizing mass tagging reagents comprising a non-encoded detectable label

Development of a CDC-certified total testosterone assay for adult and pediatric samples using LC-MS/MS.

A method is described for mass spectrometric analysis, detection and quantification of catecholamines. The methods can comprise reacting the catecholamines with a 4- aminoantippyrine reagent and detecting and/or quantifying the adduct produced by the reaction. The methods can also allow for multiplexing. Compounds formed by the reactions are also provided.

Subhakar Dey

Papers

Methods, compositions and libraries pertaining pna dimer and pna oligomer synthesis

Composition, method, and kit for calibrating a mass spectrometer

Analyte determination utilizing mass tagging reagents comprising a non-encoded detectable label

Development of a CDC-certified total testosterone assay for adult and pediatric samples using LC-MS/MS.

Mass spectrometric identification and/or quantitation of catecholamines using aminopyrazoles