A public repository for mass spectrometry imaging data.
A public repository for mass spectrometry imaging data.
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DOI：
10.1007/s00216-014-8357-8
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发表时间：
2015-03
影响因子：
4.3
通讯作者：
Vizcano, Juan Antonio
中科院分区：
文献类型：
--
作者：
Roempp, Andreas;Wang, Rui;Albar, Juan Pablo;Urbani, Andrea;Hermjakob, Henning;Spengler, Bernhard;Vizcano, Juan Antonio
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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
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影响因子：
14.9
作者：
Haug K;Salek RM;Conesa P;Hastings J;de Matos P;Rijnbeek M;Mahendraker T;Williams M;Neumann S;Rocca-Serra P;Maguire E;González-Beltrán A;Sansone SA;Griffin JL;Steinbeck C
通讯作者：
Steinbeck C
DOI：
10.1093/database/bat009
发表时间：
2013
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Mayer G;Montecchi-Palazzi L;Ovelleiro D;Jones AR;Binz PA;Deutsch EW;Chambers M;Kallhardt M;Levander F;Shofstahl J;Orchard S;Vizcaíno JA;Hermjakob H;Stephan C;Meyer HE;Eisenacher M;HUPO-PSI Group
通讯作者：
HUPO-PSI Group
DOI：
10.1007/s13361-012-0572-y
发表时间：
2013-04
影响因子：
3.2
作者：
Parry RM;Galhena AS;Gamage CM;Bennett RV;Wang MD;Fernández FM
通讯作者：
Fernández FM
影响因子：
3.3
作者：
Schramm, Thorsten;Hester, Alfons;Roempp, Andreas
通讯作者：
Roempp, Andreas
影响因子：
14.9
作者：
Vizcaíno JA;Côté RG;Csordas A;Dianes JA;Fabregat A;Foster JM;Griss J;Alpi E;Birim M;Contell J;O'Kelly G;Schoenegger A;Ovelleiro D;Pérez-Riverol Y;Reisinger F;Ríos D;Wang R;Hermjakob H
通讯作者：
Hermjakob H