<tt>masstodon</tt>: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry

Łącki, Mateusz Krzysztof; Lermyte, Frederik; Miasojedow, Błażej; Startek, Michał; Sobott, Frank; Valkenborg, Dirk; Gambin, Anna

doi:10.1021/acs.analchem.8b01479

Cited by 7 publications

(2 citation statements)

References 57 publications

(126 reference statements)

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“…It is notably faster than other approaches and can be used both for scripting and in development of professional software for raw data analysis. The IsoSpec algorithm has found application in a variety of projects. ,− It is open-source, can be used on a variety of operating systems (Linux, MacOS, Windows), and is available for download from github, PyPI, and CRAN.…”

Section: Resultsmentioning

confidence: 99%

IsoSpec2: Ultrafast Fine Structure Calculator

2020

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High-resolution mass spectrometry becomes increasingly available with its ability to resolve the fine isotopic structure of measured analytes. It allows for high-sensitivity spectral deconvolution, leading to less false-positive identifications. Analytes can be identified by comparing their theoretical isotopic signal with the observed peaks. Necessary calculations are, however, computationally demanding and lead to long processing times. For wheat (trictum oestivum) alone, Uniprot holds more than 142 000 candidate protein sequences. This is doubled upon sequence reversal for identification FDR estimation and further multiplied by performing in silico digestion into peptides. The same peptide might originate from more than one protein, which reduces the overall number of sequences to be calculated. However, it is still huge. IsoSpec2 can perform these calculations fast. Compared to IsoSpec1, the algorithm is simpler, orders of magnitude faster, and offers more flexibility for the developers of algorithms for raw data analysis. It is freely available under a 2-clause BSD license, with bindings for the C++, C, R, and Python programming languages.

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Section: Resultsmentioning

confidence: 99%

IsoSpec2: Ultrafast Fine Structure Calculator

2020

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“…YADA 23 was designed to handle highly charged middle-down tandem mass spectrometry (MS/MS) data. While most tools use the Averagine model 24 to estimate chemical compositions of ions, ProteinGoggle 25 and masstodon 26 use chemical compositions of proteoforms and proteoform fragments from which mass spectra were generated to increase the accuracy of spectral deconvolution. In spectral deconvolution, an isotopic envelope in a mass spectrum is converted into a monoisotopic mass with the following steps.…”

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confidence: 99%

EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-Spectral Deconvolution

2020

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Top-down mass spectrometry has become the main method for intact proteoform identification, 14 characterization, and quantitation. Because of the complexity of top-down mass spectrometry 15 data, spectral deconvolution is an indispensable step in spectral data analysis, which groups 16 spectral peaks into isotopic envelopes and extracts monoisotopic masses of precursor or 17 fragment ions. The performance of spectral deconvolution methods relies heavily on their 18 scoring functions, which distinguish correct envelopes from incorrect ones. A good scoring 19 function increases the accuracy of deconvoluted masses reported from mass spectra. In this 20 paper, we present EnvCNN, a convolutional neural network-based model for evaluating isotopic 21 envelopes. We show that the model outperforms other scoring functions in distinguishing correct 22 envelopes from incorrect ones and that it increases the number of identifications and improves 23 the statistical significance of identifications in top-down spectral interpretation. 24

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Masserstein: Linear regression of mass spectra by optimal transport

Ciach

Miasojedow

Skoraczyński

et al. 2021

Rapid Comm Mass Spectrometry

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RationaleThe linear regression of mass spectra is a computational problem defined as fitting a linear combination of reference spectra to an experimental one. It is typically used to estimate the relative quantities of selected ions. In this work, we study this problem in an abstract setting to develop new approaches applicable to a diverse range of experiments.MethodsTo overcome the sensitivity of the ordinary least‐squares regression to measurement inaccuracies, we base our methods on a non‐conventional spectral dissimilarity measure, known as the Wasserstein or the Earth Mover's distance. This distance is based on the notion of the cost of transporting signal between mass spectra, which renders it naturally robust to measurement inaccuracies in the mass domain.ResultsUsing a data set of 200 mass spectra, we show that our approach is capable of estimating ion proportions accurately without extensive preprocessing of spectra required by other methods. The conclusions are further substantiated using data sets simulated in a way that mimics most of the measurement inaccuracies occurring in real experiments.ConclusionsWe have developed a linear regression algorithm based on the notion of the cost of transporting signal between spectra. Our implementation is available in a Python 3 package called masserstein, which is freely available at https://github.com/mciach/masserstein.

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`masstodon`: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry

Cited by 7 publications

References 57 publications

IsoSpec2: Ultrafast Fine Structure Calculator

IsoSpec2: Ultrafast Fine Structure Calculator

EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-Spectral Deconvolution

Masserstein: Linear regression of mass spectra by optimal transport

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masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry

Cited by 7 publications

References 57 publications

IsoSpec2: Ultrafast Fine Structure Calculator

IsoSpec2: Ultrafast Fine Structure Calculator

EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-Spectral Deconvolution

Masserstein: Linear regression of mass spectra by optimal transport

Contact Info

Product

Resources

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`masstodon`: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry