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Publications in 2008

Thesis

1. Mostaguir, K., Managing and Publishing Proteomics Data - The Make2D-DB II Tool, an Integrative Environment Applied to 2-DE Datasets. 2008, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

2. Quandt, A., swissPIT: A Grid-based analysis platform for workflow oriented mining of mass spectra. 2008, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

Journal Articles

1. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F., The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server. Journal of Proteomics, 2008. 71(2): p. 245-248.

2. Hoogland, C., Walther, D., Palagi, P.M., Bouchet, G., Mostaguir, K., Robin, X., Appel, R.D., and Lisacek, F., A suite of tools to analyse and publish 2-DE data. Proteomics., 2008. 8(23-24): p. 4907-4909.

3. Quandt, A., Hernandez, P., Masselot, A., Hernandez, C., Maffioletti, S., Pautasso, C., Appel, R.D., and Lisacek, F., swissPIT: A novel approach for pipelined analysis of mass spectrometry data. Bioinformatics, 2008. 24(11): p. 1416-1417.

4. Robin, X., Hoogland, C., Appel, R.D., and Lisacek, F., MIAPEGelDB, a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. Journal of Proteomics, 2008. 71(2): p. 249-251.

5. Scherl, A., Shaffer, S.A., Taylor, G.K., Hernandez, P., Appel, R.D., Binz, P.A., and Goodlett, D.R., On the benefits of acquiring peptide fragment ions at high measured mass accuracy. J Am Soc Mass Spectrom., 2008. 19(6): p. 891-901.

6. Vaezzadeh, A.R., Hernandez, C., Vadas, O., Deshusses, J.J., Lescuyer, P., Lisacek, F., and Hochstrasser, D.F., PICarver: a software tool and strategy for peptides isoelectric focusing. J Proteome.Res, 2008. 7(10): p. 4336-4345.

Journal Articles - non peer-reviewed

1. Binz, P.A., Barkovich, R., Beavis, R.C., Creasy, D., Horn, D.M., Julian, R.K., Jr., Seymour, S.L., Taylor, C.F., and Vandenbrouck, Y., Guidelines for reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol., 2008. 26(8): p. 862.

2. Dunn, M.J., Gil, C., Kleinhammer, C., Lottspeich, F., Pennington, S., Sanchez, J.C., Albar, J.P., Bini, L., Corrales, F., Corthals, G., Fountoulakis, M.M., Hoogland, C., James, P., Jensen, O.N., Jimenez, C., Jorrin-Novo, J., Kraus, H.J., Meyer, H., Noukakis, D., Palagi, P.M., Penque, D., Quinn, A., and Rabilloud, T., EuPA achieves visibility - An activity report on the first three years. Journal of Proteomics, 2008. 71(1): p. 11-18.

3. Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P.A., Borthwick, A., Cash, P., Day, B.W., Friedman, D.B., Garland, D., Gutstein, H.B., Hoogland, C., Jones, N.A., Khan, A., Klose, J., Lamond, A.I., Lemkin, P.F., Lilley, K.S., Minden, J., Morris, N.J., Paton, N.W., Pisano, M.R., Prime, J.E., Rabilloud, T., Stead, D.A., Taylor, C.F., Voshol, H., Wipat, A., and Jones, A.R., Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol., 2008. 26(8): p. 863-864.

4. Montecchi-Palazzi, L., Beavis, R., Binz, P.A., Chalkley, R.J., Cottrell, J., Creasy, D., Shofstahl, J., Seymour, S.L., and Garavelli, J.S., The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol., 2008. 26(8): p. 864-866.

5. Orchard, S., Albar, J.P., Deutsch, E.W., Binz, P.A., Jones, A.R., Creasy, D., and Hermjakob, H., Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. Proteomics., 2008. 8(20): p. 4168-4172.

6. Orchard, S., Martens, L., Tasman, J., Binz, P.A., Albar, J.P., and Hermjakob, H., 6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea. Proteomics., 2008. 8(7): p. 1331-1333.

7. Taylor, C.F., Binz, P.A., Aebersold, R., Affolter, M., Barkovich, R., Deutsch, E.W., Horn, D.M., Huhmer, A., Kussmann, M., Lilley, K., Macht, M., Mann, M., Muller, D., Neubert, T.A., Nickson, J., Patterson, S.D., Raso, R., Resing, K., Seymour, S.L., Tsugita, A., Xenarios, I., Zeng, R., and Julian, R.K., Jr., Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol., 2008. 26(8): p. 860-861.

8. Taylor, C.F., Field, D., Sansone, S.A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C.A., Binz, P.A., Bogue, M., Booth, T., Brazma, A., Brinkman, R.R., Michael, C.A., Deutsch, E.W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J.M., Hardy, N.W., Hermjakob, H., Julian, R.K., Jr., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Novere, N.L., Leebens-Mack, J., Lewis, S.E., Lord, P., Mallon, A.M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J.M., Robertson, D.G., Rocca-Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo-Lopez, J., Scheuermann, R.H., Schober, D., Smith, B., Snape, J., Stoeckert, C.J., Jr., Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J., and Wiemann, S., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol., 2008. 26(8): p. 889-896.

Guest Edition

1. Palagi, P.M. and Sanchez, J.C., Editorial. J Proteomics., 2008. 71(2): p. 210.

Abstracts & Posters

1. Ahrné, E., Müller, M., Binz, P.A., Masselot, A., and Lisacek, F. Increase Identification Rate by Combining On-the-fly Spectral Library and Sequence Searches. in HUPO 2008. 2008. Amsterdam, Nederlands.

2. Binz, P.A. The GeneBio-SIB collaborations: where Convergence and Divergence merge into successful bioinformatics. in European Bioalpine Convention. 2008. Geneva, Switzerland.

3. Binz, P.A. Protein Identification - Tools and Algorithms. in Joint BSPR/EBI Workshop - Bioinformatics for Proteomics. 2008. Hinxton, United Kingdom.

4. Binz, P.A. Strategies for protein identification: What data is in my data? in FinnProt meeting. 2008. Takho, Finland.

5. Binz, P.A. Validation approaches in protein identification: use cases with Penyx. in Proteomics Methods Forum. 2008. Dundee, United Kingdom.

6. Binz, P.A., Budin, N., Sankar, M., Müller, M., Lisacek, F., and Masselot, A. Proteomics: Data explosion under control? in 8th Siena Meeting from genome to proteome 2008. 2008. Siena, Italy.

7. Binz, P.A., Kapp, E.A., Shofstahl, J., Creasy, D., UniProt, C., Falkner, J.A., Andrews, P.C., and Seymour, S.L. A Common Sequence Database Format in Proteomics. in HUPO 8th Annual World Congress. 2008. Amsterdam, Netherlands.

8. Binz, P.A., Müller, M., Bouyssié, D., and Lisacek, F. How Stable are Peptide Identifications with Regards to Variations in MS/MS Spectra? in ASMS 2008. 2008. Denver, Colorado, USA.

9. Binz, P.A., Niknejad, A., Budin, N., Evalet, O., and Masselot, A. Validation approaches in Protein Identification with Phenyx: not only FDR. in SFEAP 2008. 2008. Tours, France.

10. Deutsch, E., Souda, P., Montecchi-Palazzi, L., Tasman, J., Binz, P.A., Hermjakob, H., and Martens, L. Design and implementations of the new Proteomics Standards Initiative's mass spectrometer output file standard format : mzML 1.0. in ASMS 2008. 2008. Denver, Colorado, USA.

11. Deutsch, E.W., Binz, P.A., Kessner, D., Chambers, M., Montecchi-Palazzi, L., Shofstahl, J., Tasman, J., Julian Jr, R.K., Levander, F., Souda, P., and Martens, L. Design and implementations of the new PSI mass spectrometer output file standard : mzML. in 8th Siena Meeting from genome to proteome 2008. 2008. Siena, Italy.

12. Deutsch, E.W., Martens, L., Tasman, J., Shofstahl, J., Kessner, D., Chambers, M., Levander, F., Souda, P., Montecchi-Palazzi, L., Hermjakob, H., and Binz, P.A. Design and implementations of the new PSI mass spectrometer output file standard: mzML 1.0. in HUPO 2008. 2008. Amsterdam, Nederlands.

13. Hochstrasser, D.F., Viette, V., Geiser, L., Farina, A., Dumonceau, J.M., Frossard, J.L., Hadengue, A., Mauron, Y., Mylonas, R., Masselot, A., Binz, P.A., Lisacek, F., Fathi, M., and Lescuyer, P. Proteomics & Clinical Chemistry. in IFCC-WorldLab 2008. 2008. Fortaleza, Brasil.

14. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F. World-2DPAGE Repository: your contribution to a large proteomics data network. in 8th Siena meeting "From genome to proteome: Integration and proteome completion". 2008. Siena, Italy.

15. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F. World-2DPAGE Repository: your contribution to a large proteomics data network. in HUPO 8th Annual World Congress. 2008. Amsterdam, Netherlands.

16. Mauron, Y., Mylonas, R., Masselot, A., Binz, P.A., Hochstrasser, D.F., and Lisacek, F. SmileMS; A New Mass Spectrometry Based Identification Platform for Small Molecules. in Swiss MedLab 2008. 2008. Montreux, Switzerland.

17. Müller, M., Binz, P.A., Bouyssi‚, D., and Lisacek, F. On the Stability Peptide Identifications when looking at Variations in MS/MS Spectra. in HUPO 2008. 2008. Amsterdam, Nederlands.

18. Robin, X., Hoogland, C., Appel, R.D., and Lisacek, F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. in HUPO 8th Annual World Congress. 2008. Amsterdam, Netherlands.

19. Robin, X., Hoogland, C., Appel, R.D., and Lisacek, F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. in 8th Siena meeting "From genome to proteome: Integration and proteome completion". 2008. Siena, Italy.

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