JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals

Tostengard

2020

J. Proteome Res.

Self Cite

Extracted ion chromatograms (XIC) are the fundamental signal unit in mass spectrometry. There are many algorithms for analyzing raw mass spectrometry data tasked with distinguishing real isotopic signals from noise. While one or more of the available algorithms are typically chained together for end-to-end mass spectrometry analysis, analysis of each algorithm in isolation provides a specific measurement of the strengths and weaknesses of each approach. Though qualitative opinions on extraction algorithm performance abound, quantitative performance has never been publicly ascertained. Quantitative evaluation has not occurred partly due to the lack of an available quantitative ground truth MS1 data set. Using a recently published, manually extracted XICs as ground truth data, we evaluate the quality of popular XIC algorithms, including MaxQuant, MZMine2, and several methods from XCMS. The manually curated data set comprises 48 human proteins stratified over 6 abundance orders of magnitude. Signals in the sample were manually curated into XIC using a commercial tool for visually identifying XIC and isotopic envelopes. XIC algorithms were applied to the manually extracted data using a grid search of possible parameters. Performance varied greatly between different parameter settings, though nearly all algorithms with parameter settings optimized with respect to the number of true positives recovered over 10 000 XICs.

Section: Metricsmentioning

confidence: 99%

Quantitative Evaluation of Ion Chromatogram Extraction Algorithms

Tostengard

2020

J. Proteome Res.

Self Cite

“… It must provide the user with efficient navigation of the data (zoom and shifting to the right, left, up, or down). JS-MS [ 7 ] is one of very few MS data tools that can be easily installed on multiple operating systems without the need for excessive dependencies or onerous compilation (another, for example, is pyOpenMS [ 8 ]).…”

Section: Introductionmentioning

confidence: 99%

“…JS-MS [7] is one of very few MS data tools that can be easily installed on multiple operating systems without the need for excessive dependencies or onerous compilation (another, for example, is pyOpenMS [8]). JS-MS is a browser-based JavaScript viewer and Java server designed to load and view MS1 data.…”

mentioning

confidence: 99%

A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data

Henning

2020

BMC Bioinformatics

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Background Mass spectrometry (MS) uses mass-to-charge ratios of measured particles to decode the identities and quantities of molecules in a sample. Interpretation of raw MS depends upon data processing algorithms that render it human-interpretable. Quantitative MS workflows are complex experimental chains and it is crucial to know the performance and bias of each data processing method as they impact accuracy, coverage, and statistical significance of the result. Creation of the ground truth necessary for quantitatively evaluating MS1-aware algorithms is difficult and tedious task, and better software for creating such datasets would facilitate more extensive evaluation and improvement of MS data processing algorithms. Results We present JS-MS 2.0, a software suite that provides a dependency-free, browser-based, one click, cross-platform solution for creating MS1 ground truth. The software retains the first version’s capacity for loading, viewing, and navigating MS1 data in 2- and 3-D, and adds tools for capturing, editing, saving, and viewing isotopic envelope and extracted isotopic chromatogram features. The software can also be used to view and explore the results of feature finding algorithms. Conclusions JS-MS 2.0 enables faster creation and inspection of MS1 ground truth data. It is publicly available with an MIT license at github.com/optimusmoose/jsms.

“…Like several other ion chromatogram extraction algorithms, XFlow forms one step in a two-step process where ion chromatograms (blue, red, green) are extracted from raw data. In the example workflow provided for the software JS-MS [8,9], the XICs are then combined into isotopic envelopes (purple). https://doi.org/10.1371/journal.pone.0227659.g002…”

Section: Introductionmentioning

confidence: 99%

XFlow: An algorithm for extracting ion chromatograms

Gutierrez

2020

PLoS ONE

Self Cite

Mass spectrometry is a fundamental tool for modern proteomics. The increasing availability of mass spectrometry data paired with the increasing sensitivity and fidelity of the instruments necessitates new and more potent analytical methods. To that end, we have created and present XFlow, a feature detection algorithm for extracting ion chromatograms from MS1 LC-MS data. XFlow is a parameter-free procedurally agnostic feature detection algorithm that utilizes the latent properties of ion chromatograms to resolve them from the surrounding noise present in MS1 data. XFlow is designed to function on either profile or centroided data across different resolutions and instruments. This broad applicability lends XFlow strong utility as a one-size-fits-all method for MS1 analysis or target acquisition for MS2. XFlow is written in Java and packaged with JS-MS, an open-source mass spectrometry analysis toolkit.