Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools. Here we have developed massPix - an R package for analysing and interpreting data from MSI of lipids in tissue. MassPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications. MassPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries. Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering. Mouse cerebellum was analysed using matrix assisted laser desorption ionisation (MALDI) MSI. The resulting MSI dataset forms the test data for massPix.

The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows, including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.

Replication data for the publication: "rSIREM: an R package for MALDI spectral deconvolution" by Del Castillo Pérez et al. The deposited data are SALDI-MSI data of three consectutive thin tissue sections from mouse cerebellum measured at the different mass resolutions at the same instrument (MALDI-MSI: Spectroglyph Injector - Orbitrap Exploris). The paper describes a new R package (rSIREM) to computationally improve the mass resolution of an MSI post-measurement. The developed R package (https://github.com/EdelCastillo/rSirem ) applies a statistical treatment on the concentration of spatial images obtained by separately considering each of the m/z over all the pixels. A representative scalar is associated with each image, obtained by applying a new measure (SIREM) to it, derived from Shannon's entropy. The perturbations of this measure, when considering a sequence of consecutive images, reveal the existence of overlap, if it exists. This information serves as a seed to initialize the EM algorithm in the Gaussian Mixture Model context. The efficiency of the method has been verified using three independent procedures.

With recent advances in analytical chemistry, liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS) has become an essential tool for metabolite discovery and detection. Even if most of the common drug transformations have already been extensively described, manual search of drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology laboratories, complicating metabolite discovery. Furthermore, the availability of free open-source software for metabolite discovery is still limited. In this article, we present MetIDfyR, an open-source and cross-platform R package for in silico drug phase I/II biotransformation prediction and mass-spectrometric data mining. MetIDfyR has proven its efficacy for advanced metabolite identification in semi-complex and complex mixtures in in vitro or in vivo drug studies and is freely available at github.com/agnesblch/MetIDfyR.

Supporting datasets and algorithms (R-based) for the manuscript entitled "Development of a Tool to Determine the Variability of Consensus Mass Spectra", including an R Markdown script to reproduce the manuscript's figures.

The repository contains three mzML and four imzML mass spectrometry datasets,

The mzML data are compiled in a single directory 'mzML' and zipped:

• Col_1.mzML is a liquid chromatography (LC) ESI MS dataset from an Arabidopsis extraction published in: Sotelo-Silveira, M., Chauvin, A.-L., Marsch-Martínez, N., Winkler, R. & De Folter, S. Metabolic fingerprinting of Arabidopsis thaliana accessions. Frontiers in Plant Science 6, 1–13 (2015). https://doi.org/10.3389/fpls.2015.00365.
• Cytochrome_C.mzML is an electrospray mass spectrometry (ESI MS) dataset of Cytochrome C. The data were discussed in: Winkler, R. ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data. Rapid Communications in Mass Spectrometry 24, 285- 294 (2010). https://doi.org/10.1002/rcm.4384.
• T9_A1.mzML is a low-temperature plasma (LTP) MS dataset of the interaction between Arabidopsis and Trichoderma, published in 1. Torres-Ortega, R. et al. In Vivo Low-Temperature Plasma Ionization Mass Spectrometry (LTP-MS) Reveals Regulation of 6-Pentyl-2H-Pyran-2-One (6-PP) as a Physiological Variable during Plant-Fungal Interaction. Metabolites 12, 1231 (2022). https://doi.org/10.3390/metabo12121231.

The imzML mass spectrometry imaging data are zipped individually:

• imzML_AP_SMALDI.zip contains an AP-SMALDI mass spectrometry imaging data set of mouse urinary bladder slides, published by Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B., ProteomeXchange dataset PXD001283. 2014., and available from https://www.ebi.ac.uk/pride/archive/projects/PXD001283; Publication: Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B; Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging., Angew Chem Int Ed Engl, 49, 22, 3834-8 (2014). https://doi.org/10.1002/anie.200905559, PubMed: 20397170.
• imzML_DESI.zip is a DESI mass spectrometry imaging data set of human colorectal cancer tissue by Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein PC, Takats Z, Alexandrov T. 2015. Benchmark datasets for 3D MALDI-and DESI-imaging mass spectrometry. GigaScience 4(1):2105 https://doi.org/10.1186/s13742-015-0059-4.
• imzML_LA-ESI.zip is an LA-ESI mass spectrometry imaging data set of an Arabidopsis thaliana leaf by Zheng, Z., Bartels, B., & Svatoš, A. (2020). Laser Ablation Electrospray Ionization Mass Spectrometry Imaging (LAESI MSI) of Arabidopsis thaliana leaf [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3678473.
• imzML_LTP.zip was generated by low-temperature plasma ionization ambient mass spectrometry imaging of a chili fruit, published by Maldonado-Torres M, López-Hernández Jé F, Jiménez-Sandoval P, Winkler R. 2014. Plug and play' assembly of a low-temperature plasma ionization mass spectrometry imaging (LTP-MSI) system. Journal of Proteomics 102C:60–65 https://doi.org/10.1016/j.jprot.2014.03.003; Mauricio Maldonado-Torres, José Fabricio López-Hernández, Pedro Jiménez-Sandoval, & Robert Winkler. (2017). Low-temperature plasma mass spectrometry imaging (LTP-MSI) of Chili pepper [Data set]. In Journal of proteomics (Vol. 102, pp. 60–65). Zenodo. https://doi.org/10.5281/zenodo.484496.

All these datasets are publicly available from different repositories; however, If you reuse them, please attribute the original authors!

Motivation

Estimating the properties of galaxies, and even where they are, is a challenging process. The Rubin Observatory, a sky survey telescope located in Chile, will once it becomes operational image tens of billions of astronomical objects, the vast majority of which will be galaxies that have never been imaged before. Analyses of these data will require sophisticated methodologies, ones that will allow us to first determine where the galaxies are (i.e., how far away they are), and then conditional on the distance, how massive they are. Given galaxy distance and mass data, we can test theories of how the Universe evolves, by comparing simulated galaxy data with these data.

The Buzzard-V1.0 simulation was used to generate a realistic sample of Rubin Observatory data. In this dataset are measurements for 111,172 galaxies. Developers used these data to benchmark, e.g., methods for estimating galaxy distance. Here, we can assume the distance has been estimated well, and use these data to try to model galaxy mass as a function of brightness and distance.

Data

The dataset contains measures of magnitude and magnitude uncertainty in six astronomical bands (u for ultraviolet, g for green, r for red, i for infrared, and z and y for two additional infrared bands). Magnitude is a logarithmic measure of brightness, with an increase of 5 representing a decrease in brightness by a factor of 100, and with a value of zero being represented (roughly) by how the star Vega appears in the night sky. In addition, there is a redshift measured for each galaxy; it represents by how much light from the galaxy is stretched (by the expansion of Universe) as it travels to us. Thus higher redshifts represent larger distances. The last measurement is log.mass, which is the base-10 logarithm of the galaxy stellar mass in units of solar mass; for instance, log.mass = 10 means that the galaxy has a mass 10 billion times that of the Sun.

Variable Description

• u Galaxy magnitude in Rubin u band (320.5-393.5 nm)
• g Galaxy magnitude in Rubin g band (401.5-551.9 nm)
• r Galaxy magnitude in Rubin r band (552.0-691.0 nm)
• i Galaxy magnitude in Rubin i band (691.0-818.0 nm)
• z Galaxy magnitude in Rubin z band (818.0-923.5 nm)
• y Galaxy magnitude in Rubin y band (923.8-1084.5 nm)
• u.err Uncertainty for u-band magnitude
• g.err Uncertainty for g-band magnitude
• r.err Uncertainty for r-band magnitude
• i.err Uncertainty for i-band magnitude
• z.err Uncertainty for z-band magnitude
• y.err Uncertainty for y-band magnitude
• log.mass Galaxy stellar mass (log-base-10 solar masses)
• redshift Galaxy redshift

Questions

As noted above, the idea here is to learn a statistical association between measures of magnitude and distance, and galaxy mass.

One wrinkle here that analysts can exploit is that the data contain standard error estimates for the magnitudes (though not for redshift, for which, in practice, the error would be ).

References

Schmidt, Malz, Soo, Almosallam, Brescia, Cavuoti, Cohen-Tanugi, Connolly, DeRose, Freeman, Graham, Iyer, Jarvis, Kalmbach, Kovacs, Lee, Longo, Morrison, Newman, Nourbakhsh, Nuss, Pospisil, Tranin, Wechsler, Zhou, Izbicki, (The LSST Dark Energy Science Collaboration). “Evaluation of probabilistic photometric redshift estimation approaches for The Rubin Observatory Legacy Survey of Space and Time (LSST)”. Monthly Notices of the Royal Astronomical Society 499, December 2020, pages 1587–1606. https://doi.org/10.1093/mnras/staa2799

Acknowledgement

Foto from unsplash

In the field of proteomics, generating biologically relevant results from mass spectrometry (MS) signals remains a challenging task. This is partly due to the fact that the computational strategies for converting MS signals into biologically interpretable data depend heavily on the MS acquisition method. Additionally, the processing and the analysis of these data vary depending on whether the proteomic experiment was performed with or without labeling, and with or without fractionation. Several R packages have been developed for processing and analyzing MS data, but they only incorporate identification and quantification data; none of them takes into account other invaluable information collected during MS runs. To address this limitation, we introduce MCQR, an alternative R package for the in-depth exploration, processing, and analysis of quantitative proteomics data generated from either data-dependent or data-independent acquisition methods. MCQR leverages experimental retention time measurements for quality control, data filtering, and processing. Its modular architecture offers flexibility to accommodate various types of proteomics experiments, including label-free, label-based, fractionated, or those enriched for specific post-translational modifications. Its functions, designed as simple building blocks, are user-friendly, making it easy to test parameters and methods, and to construct customized analysis scenarios. These unique features position MCQR as a comprehensive toolbox, perfectly suited to the specific needs of MS-based proteomics experiments.

This dataset is about: (Appendix 2) Compilation of mass accumulation rates from deep sea sediments during the Holocene. Please consult parent dataset @ https://doi.org/10.1594/PANGAEA.726364 for more information.

This dataset contains aerosol gravimetric analysis of mass, using 2-stage multi-jet cascade impactors, taken aboard the Ron Brown ship during the ACE-Asia field project. This dataset contains the tab delimited (.acf) data files. Data can also be downloaded in a netCDF format.

This dataset is about: (Appendix 2) Compilation of mass accumulation rates from deep sea sediments during the last glacial maximum. Please consult parent dataset @ https://doi.org/10.1594/PANGAEA.726364 for more information.

Our aim is to identify the population of very low-mass object (VLMO) candidates in the R CrA region and reveal their formation dependence in the local environments. We performed a deep near-infrared (NIR) photometric observation of the R CrA region by UKIRT/WFCAM. Class I and II candidates showing NIR excess were selected from their observed colors. We derived the photometric mass of each candidate with an age assumption of 1Myr. We compared the derived mass of identified VLMO candidates to the dust column density at their position. The 10{sigma} limiting magnitudes were 20.7, 19.6, and 19.2mag in the J-, H-, and K-band, respectively, and we detected 2922 JHK sources in all three bands with an S/N greater than ten in the K-band. Fifteen Class I and 207 Class II candidates with NIR excess were selected from a [J-H]/[H-K] color-color diagram. Six low-mass stars, five brown dwarfs, and 196 planetary-mass object candidates were identified from the J-band luminosity of Class II candidates with the age assumption of 1 Myr using the evolutionary models. The derived initial mass function (IMF) does not appear to decrease in the brown dwarf and planetary-mass regime, even when taking into account the background star and galactic contamination. From comparison between the spatial distributions of Class I and II candidates and dust column densities derived from the Herschel observation, we found that all the low-mass star and brown dwarf candidates are located in the region where the dust column densities are higher than 2.5x10^21^cm^-2^, while planetary-mass object candidates are independent of their local dust densities. Our results suggest that the formations of low-mass stars and very low-mass objects may be dependent on the local cloud properties.

Scripts for analysis of DI-qTOF data recorded for studies of refractory dissolved organic matter

Requisite R files for the Proteo-SAFARI app

Additional file 1: Publication analysis code. Analysis code to reproduce present study.

Contains the parameters/set-up for a VIC model run along with the input and post-processed output from the model along with a python notebook to recreate the figures in the GRL paper of the same name.

Datasets and R scripts from González-Suárez, M; Gonzalez-Voyer, A; von Hardenberg, A; Santini, L (2021) The role of brain size on mammalian population densities Journal of Animal Ecology, 90: 653– 661. DOI: 10.1111/1365-2656.13397Additional details in the README.pdf file

SUMMARY OF FILES INCLUDED

• CSV datasets: total 21 files representing

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12 csv datasets from other sources (described below) with brain and body mass data in the zip file Brain and Mass data.

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Six csv datasets from other sources and compilations (described below) with population density and diet information

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Two csv files (Complete_dataset_published.csv, Brain_data_compilation_published.csv) produced during this study. Details of the files and the compilation protocol are provided in the README file.

• R scripts: three scripts that describe the protocols to: combine brain and body mass data (brain_data_compilation_published.Rmd), combine all sources (Joining_all_data_published.Rmd), and analyse and produce tables and figures presented in the manuscript (Data_analysesPPA_published.Rmd).

SOIREE Sediment Traps - Total Mass Flux

. Visit https://dataone.org/datasets/sha256%3A2c31a8029059075ca1ab79991d6de232cb2c8c83650aeb1534b5245273f1feb4 for complete metadata about this dataset.

A major bottleneck of mass spectrometric metabolomic analysis is still the rapid detection and annotation of unknown m/z features across biological matrices. This kind of analysis is especially cumbersome for complex samples with hundreds to thousands of unknown features. Traditionally, the annotation was done manually imposing constraints in reproducibility and automatization. Furthermore, different analysis tools are typically used at different steps which requires parsing of data and changing of environments. We present here MetNet, implemented in the R programming language and available as an open-source package via the Bioconductor project. MetNet, which is compatible with the output of the xcms/CAMERA suite, uses the data-rich output of mass spectrometry metabolomics to putatively link features on their relation to other features in the data set. MetNet uses both structural and quantitative information on metabolomics data for network inference and enables the annotation of unknown analytes.

Supplemental Data for R analyses; each sheet should be saved out as its own .csv for R. This file is missing the humerus and femur circumference metrics. All analyses as in the R file will still run, but data is important! It is included in version 2.