MAX PRINCIPLE AND UNIVERSAL SPECTRUM OF PERIODS: COMPLEMENTARY FRACTAL DISTRIBUTIONS AS CONSEQUENCE OF RATIONAL AND IRRATIONAL RELATIONS BETWEEN PARTS OF THE WHOLE SYSTEM

The paper discusses the assumption that Mach principle should result in existence of a universal spectrum of periods. It is shown that fragments of such a spectrum were found in time series of fluctuations of various processes. A general approach is considered that demonstrates the emergence of discrete states in the spectra of periods, which is based on two basic concepts: resonance and roughness of a physical system. This approach leads to the existence of two complementary fractal distributions associated with sets of rational and irrational relations between the elements of the whole system. A brief review of works that also consider universal spectra of periods is given.

Universal Spectrum Identifier for mass spectra

The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USIs enable greater transparency for providing spectral evidence in support of key findings in publications, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

On external influences on the radioactive decay rate fluctuations

The evolution of views on the possibility of external influence on the process of radioactive decay is briefly presented. Such an effect can lead to the appearance of periods in the time series of the radioactive decay rate fluctuations, which have been the subject of intensive study in the last decade. Two mechanisms for identifying periods are considered: the study of deviations from the theoretical curve of the radioactive decay law and the study of the properties of fluctuations. It is shown that the latter method leads to a universal spectrum of periods observed not only in the time series of the radioactive decay rate fluctuations, but also in the time series of fluctuations of processes of various nature. The main object of our study are periods in the radioactive decay rate fluctuations. The presence of such periods suggests the possibility of external influence on the process of radioactive decay. Therefore, we briefly consider the evolution of views on the possibility of such an effect. To do this, we distinguish several stages. The division into stages is only partially historical, but, mainly, each stage characterizes a certain ideas that is implemented in it.

On the universal spectrum of periods in the time series of temperature fluctuations in starlings and rats

The paper considers a spectral analysis based on Fourier transform of the time series in the temperature fluctuations in the bodies of common starlings (Sturnus vulgaris) and rats (mature Wistar males). The spectra of the periods in the starlings and rats contain the same sets of harmonics, so on this basis we can tell about a common spectrum. Interesting to note that the spectrum coincides with a previously revealed spectrum of the periods, obtained with the use of local fractal analysis by the all permutations method in the course of studies of time series of the alpha decay rate fluctuations. Despite different methods of the experimental data processing used in this work (spectral analysis based on Fourier transform and local fractal analysis by the all permutations method), as well as different raw experimental data (the temperature fluctuations and alpha-decay rate fluctuations), the same spectrum of periods was obtained. On this basis, we can consider the spectrum of periods as universal one.

Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

Here we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can either be provided manually by the user (table format), or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project. In addition, USE can retrieve real-time prediction of tandem mass spectra from the deep learning framework Prosit. Comparison results like annotated mirror spectrum plots can be exported from USE as editable scalable high quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and seamless integration into websites (https://github.com/kusterlab/universal_spectrum_explorer).

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

The growth of online mass spectrometry metabolomics resources, including data repositories, spectral library databases, and online analysis platforms has created an environment of online/web accessibility. Here, we introduce the Metabolomics Spectrum Resolver (https://metabolomics-usi.ucsd.edu/), a tool that builds upon these exciting developments to allow for consistent data export (in human and machine-readable forms) and publication-ready visualisations of tandem mass spectrometry spectra. This tool supports the Human Proteome Organization – Proteomics Standards Initiative’s Universal Spectrum Identifier (USI) specification, which has been extended to deal with the metabolomics use cases. To date, this resource already supports data formats from GNPS, MassBank, MS2LDA, MassIVE, MetaboLights, and Metabolomics Workbench and is integrated into several of these resources.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20,000 human proteins encoded by the human genome.Abstract Figure