A public repository for mass spectrometry imaging data

Analytical and Bioanalytical Chemistry

Volumn 407, Issue 8, 2015, Pages 2027-2033

  Römpp, Andreas ^a   Wang, Rui ^b   Albar, Juan Pablo ^c   Urbani, Andrea ^d,e   Hermjakob, Henning ^b   Spengler, Bernhard ^a   Vizcaíno, Juan Antonio ^b  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^d UNIVERSITY OF ROME TOR VERGATA   (Italy)

^e IRCCS FONDAZIONE SANTA LUCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MASS SPECTROMETRY; PROTEOMICS;

COMMAND LINE; COMMON DATUM; IMAGING DATA; MASS-SPECTROMETRY IMAGING; PUBLIC INVESTMENTS; PUBLIC REPOSITORIES; REVIEWING PROCESS;

INVESTMENTS;

ANIMAL; DIAGNOSTIC IMAGING; FACTUAL DATABASE; HUMAN; MASS SPECTROMETRY; SOFTWARE;

ANIMALS; DATABASES, FACTUAL; DIAGNOSTIC IMAGING; HUMANS; MASS SPECTROMETRY; SOFTWARE;

EID: 84936858024     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-014-8357-8     Document Type: Review

References (21)

1. Römpp A, Spengler B (2013) Mass spectrometry imaging with high resolution in mass and space. Histochem Cell Biol 139(6):759-783
2. Chughtai K, Heeren RMA (2010) Mass spectrometric imaging for biomedical tissue analysis. Chem Rev 110(5):3237-3277
3. Taylor CF, Binz P-A, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Huhmer A, Kussmann M, Lilley K, Macht M, Mann M, Muller D, Neubert TA, Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I, Zeng R, Julian RK (2008) Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol 26(8):860-861
4. Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz P-A, Deutsch EW (2011) mzML - a community standard for mass spectrometry data. Mol Cell Proteomics. doi: 10.1074/mcp.R1110.000133
5. Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino JA (2014) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics. doi: 10.1002/pmic.201400302
6. 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 S-A, Griffin JL, Steinbeck C (2013) MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 41(D1):D781-D786
7. Craig R, Cortens JP, Beavis RC (2004) Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 3(6):1234-1242
8. Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res 13(1):60-75
9. Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41(D1):D1063-D1069
10. Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz P-A, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus H-J, Albar JP, Martinez-Bartolome S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32(3):223-226
11. Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprévote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Römpp A (2012) imzML - a common data format for the flexible exchange and processing of mass spectrometry imaging data. J Proteome 75(16):5106-5110
12. McDonnell LA, Römpp A, Balluff B, Heeren RMA, Albar JP, Andren P, Corthals G, Walch A, Stoeckli M (2014). Discussion point: reporting guidelines for mass spectrometry imaging. Anal Bioanal Chem. doi: 10.1007/s00216-014-8322-6
13. Ternent T, Csordas A, Qi D, Gomez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaino JA (2014) How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics. doi: 10.1002/pmic.201400120
14. Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B (2010) Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging. Angew Chem Int Ed 49(22):3834-3838
15. Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaino JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M (2013) The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database. doi: 10.1093/database/bat009
16. Robichaud G, Garrard K, Barry J, Muddiman D (2013) MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform. J Am Soc Mass Spectrom 24(5):718-721
17. Klinkert I, Chughtai K, Ellis SR, Heeren RMA (2014) Methods for full resolution data exploration and visualization for large 2D and 3D mass spectrometry imaging datasets. Int J Mass Spectrom 362(1):40-47
18. Parry RM, Galhena A, Gamage C, Bennett R, Wang M, Fernández F (2013) OmniSpect: an open MATLAB-based tool for visualization and analysis of matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry images. J Am Soc Mass Spectrom 24(4):646-649
19. Imabiotech (2012) Quantinetix MALDI imaging software. http://www.imabiotech.com/Quantinetix-TM-Maldi-Imaging.html?lang=en. Accessed 8 Jul 2012
20. PREMIERBiosoft (2012) MALDIVision. http://www.premierbiosoft.com/maldi-tissue-imaging/index.html. Accessed 3 Jul 2012
21. Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B (2014) Mass-spectrometry-based draft of the human proteome. Nature 509(7502):582-587