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DNA Packaging

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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...

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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
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Chromatin Packaging

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Integrals involving non-rational functions are often difficult to evaluate using standard techniques, especially when radicals appear in the integrand. Rationalizing substitution provides a systematic method for simplifying such integrals by converting them into rational forms that are easier to handle.Consider a rod whose linear mass density depends on a constant linear density, a characteristic length, and the distance from the left end of the rod. Determining the total mass requires...

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Skeletal Muscle Gender Dimorphism from Proteomics

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rawDiag: An R Package Supporting Rational LC-MS Method Optimization for Bottom-up Proteomics.

Christian Trachsel¹, Christian Panse¹, Tobias Kockmann¹

¹Functional Genomics Center Zurich, Swiss Federal Institute of Technology Zurich , University of Zurich , Winterthurerstr. 190 , CH-8057 Zurich , Switzerland.

Journal of Proteome Research

|July 7, 2018

Summary

rawDiag is a new software tool that simplifies optimizing liquid chromatography-mass spectrometry (LC-MS) methods. It provides diagnostic plots to help mass spectrometry (MS) operators improve their methods efficiently.

Keywords:

R package mass spectrometry method optimization multiplatform quality control reproducible research visualization

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Area of Science:

Analytical Chemistry
Biotechnology
Computational Biology

Background:

Optimizing methods for liquid chromatography-mass spectrometry (LC-MS) is complex and time-consuming.
Effective LC-MS method optimization is crucial for accurate and reliable data acquisition.

Purpose of the Study:

To introduce rawDiag, a novel software tool designed to rationalize and streamline LC-MS method optimization.
To provide mass spectrometry (MS) operators with user-friendly diagnostic tools for method development.

Main Methods:

rawDiag is developed as an R package, offering both command-line and graphical user interface (GUI) options.
The software processes scan-level metadata to generate diagnostic plots tailored for MS operators.
Performance benchmarks demonstrate the tool's efficiency, processing 100 raw files in under 3 minutes on standard hardware.

Main Results:

rawDiag facilitates rational method optimization through intuitive, operator-focused diagnostic plots.
The software is platform-independent and highly efficient, significantly reducing optimization time.
A real-world example from a core facility showcases the practical application and benefits of rawDiag.

Conclusions:

rawDiag offers a powerful and efficient solution for optimizing LC-MS methods.
The tool enhances usability for both experienced and less experienced MS operators.
Implementation of rawDiag can lead to improved data quality and faster method development in core facilities.