A public repository for mass spectrometry imaging data.

Abstract

Mass spectrometry (MS) imaging is a very active field of research, and has seen impressive progress in recent years [1, 2]. The number of groups that are working on this topic is constantly increasing. However, the field is still very heterogeneous in terms of applied instrumentation and data processing methods. In addition, complex datasets are reduced to a set of two-dimensional “images,” which inevitably results in information loss. This simplified graphical representation also strongly depends on processing options such as color scale, intensity normalization, and spatial interpolation. Consequently, experimental data are presented in very diverse ways, and published results can therefore be difficult to evaluate and compare. With a growing number of published studies, the issue of standardization and quality control of MS imaging data is becoming more important. This is a natural process for any new field that is maturing. The MS-based proteomics community has been facing similar issues in the last decade, and this discipline is therefore discussed as a “role model” herein. Since its inception in 2002, the Proteomics Standards Initiative (http://www.psidev.info) has driven the development of a number of minimum reporting guidelines (called “minimum information about a proteomics experiment” documents) [3] and several standard data formats for the different data types relevant in proteomics. For example, for raw and processed MS data, the data standard is called mzML [4]. In addition, several data repositories were established about 10 years ago to address the demand for storage and availability of MS data in the public domain [5–9]. A big step forward in this area has been the establishment of the ProteomeXchange (PX; http://www.proteomexchange.org/) consortium [10], led by the PRIDE [9] and PeptideAtlas [8] resources. The overall aim of PX is to provide a common framework and infrastructure for the cooperation of proteomics resources by defining and implementing consistent, harmonized, user-friendly data deposition and exchange procedures among the members. Thanks to the guidelines promoted by several scientific journals and funding agencies, and the general perception that sharing data is good scientific practice, the culture in the proteomics community has evolved toward data deposition as part of the publication process. In analogy to these activities in the MS proteomics field, similar mechanisms have been discussed and to some extent already implemented in the MS imaging community in recent years. A common data format for MS imaging—imzML—has been established [11]. This format is being used more and more, and the number of available tools is constantly growing (see http://www.imzml.org for more details). Reporting guidelines have been discussed for several years, and a first suggestion of those is included in this topical collection [12]. Nevertheless, owing to the lack of suitable resources, a missing element so far has been the possibility to make MS imaging datasets available in the public domain. Earlier attempts to develop a data repository were abandoned mainly because of the large size of MS imaging datasets. However, nowadays very large datasets (i.e., file size on the order of a few terabytes) can also be generated in MS-based proteomic and metabolomic studies, and can be submitted to established repositories. From a purely technical point of view, the infrastructure available in existing MS repositories is also suited for MS imaging data. Therefore, the missing step is to define and adopt a submission procedure in order to be compatible with MS-imaging-specific parameters. Here we describe the newly implemented way of submitting MS imaging data to PX via the PRIDE database. We also describe how to retrieve these data and to reproduce the MS images.