MARMoSET - Extracting Publication-ready Mass Spectrometry Metadata from RAW Files.

Marina Kiweler,Mario Looso,Johannes Graumann

doi:10.1074/mcp.tir119.001505

Abstract

In the context of publishing data sets acquired by mass spectrometry or works based on such molecular screens, metadata documenting the instrument settings are of central importance to the evaluation and reproduction of results. A single experiment may be linked to hundreds of data acquisitions, which are frequently stored in proprietary file formats. Together with community-, repository-, as well as publisher-specific reporting standards, this state of affairs frequently leads to manual -and thus error prone-metadata extraction and formatting. Data extracted from a single file also often stand in for an entire file set, implying a risk for unreported parameter divergence. To support quality control and data reporting, the C# application MARMoSET extracts and reduces publication relevant metadata from Thermo Fischer Scientific RAW files. It is integrated with an R package for easy reporting. The tool is expected to be particularly useful to high throughput environments such as service facilities with large project numbers and/or sizes.

Highlights

In the context of publishing data sets acquired by mass spectrometry or works based on such molecular screens, metadata documenting the instrument settings are of central importance to the evaluation and reproduction of results
Aiming for evaluability and reproducibility of mass spectrometry based research and in parallel to the maturation of the field toward the acquisition of ever larger data sets, initiatives to standardize reporting of instrument settings and other relevant metadata have arisen in the community itself [1, 2], from the deposition requirements of public data repositories [3, 4], as well as have been launched by publishers and editors involved in the dissemination of mass spectrometric experiments [5, 6]
To provide easy and intuitive handling of the structured data in the JSON file, we provide an R [8] package named MARMoSET

Summary

Introduction

In the context of publishing data sets acquired by mass spectrometry or works based on such molecular screens, metadata documenting the instrument settings are of central importance to the evaluation and reproduction of results. To support quality control and data reporting, the C# application MARMoSET extracts and reduces publication relevant metadata from Thermo Fischer Scientific RAW files.

Results

Conclusion