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1. Guidelines for the next 10 years of proteomics

Author

Wilkins, Marc R, Appel, Ron D, Van Eyk, Jennifer E, Chung, Maxey C M, Görg, Angelika, Hecker, Michael, Huber, Lukas A, Langen, Hanno, Link, Andrew J, Paik, Young-Ki, Patterson, Scott D, Pennington, Stephen R, Rabilloud, Thierry, Simpson, Richard J, Weiss, Walter, and Dunn, Michael J

Subjects
Quantitative Biology - Genomics
Abstract

In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of stringency required in proteomic data generation and analysis appears to have been underestimated. As a result, there are likely to be numerous published findings that are of questionable quality, requiring further confirmation and/or validation. This manuscript outlines a number of key issues in proteomic research, including those associated with experimental design, differential display and biomarker discovery, protein identification and analytical incompleteness. In an effort to set a standard that reflects current thinking on the necessary and desirable characteristics of publishable manuscripts in the field, a minimal set of guidelines for proteomics research is then described. These guidelines will serve as a set of criteria which editors of PROTEOMICS will use for assessment of future submissions to the Journal.

Published
2009
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2. Ten Years of the Proteome

Author

Wilkins, Marc R., Appel, Ron D., Wilkins, Marc R., editor, Appel, Ron D., editor, Williams, Keith L., editor, and Hochstrasser, Denis F., editor

Published
2007
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3. Proteome Imaging

Author

Palagi, Patricia M., Walther, Daniel, Zimmermann-Ivol, Catherine G., Appel, Ron D., Wilkins, Marc R., editor, Appel, Ron D., editor, Williams, Keith L., editor, and Hochstrasser, Denis F., editor

Published
2007
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15. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Author

Stockinger, Heinz, Altenhoff, Adrian M., Arnold, Konstantin, Bairoch, Amos, Bastian, Frederic, Bergmann, Sven, Bougueleret, Lydie, Bucher, Philipp, Delorenzi, Mauro, Lane, Lydie, Le Mercier, Philippe, Lisacek, Frédérique, Michielin, Olivier, Palagi, Patricia M., Rougemont, Jacques, Schwede, Torsten, von Mering, Christian, van Nimwegen, Erik, Walther, Daniel, Xenarios, Ioannis, Zavolan, Mihaela, Zdobnov, Evgeny M., Zoete, Vincent, and Appel, Ron D.

Published
2014
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17. Characterization of protein cross-links via mass spectrometry and an open-modification search strategy

Author

Singh, Pragya, Shaffer, Scott A., Scherl, Alexander, Holman, Carol, Pfuetzner, Richard A., Freeman, Theodore J. Larson, Miller, Samuel I., Hernandez, Patricia, Appel, Ron D., and Goodlett, David R.

Subjects
Mass spectrometry -- Methods, Protein-protein interactions -- Research, Proteins -- Crosslinking, Proteins -- Research, Chemistry
Abstract

Protein--protein interactions are key to function and regulation of many biological pathways. To facilitate characterization of protein--protein interactions using mass spectrometry, a new data acquisition/analysis pipeline was designed. The goal for this pipeline was to provide a generic strategy for identifying cross-linked peptides from single LC/MS/MS data sets, without using specialized cross-linkers or custom-written software. To achieve this, each peptide in the pair of cross-linked peptides was considered to be 'post-translationally' modified with an unknown mass at an unknown amino acid. This allowed use of an open-modification search engine, Popitam, to interpret the tandem mass spectra of cross-linked peptides. False positives were reduced and database selectivity increased by acquiring precursors and fragments at high mass accuracy. Additionally, a high-charge-state-driven data acquisition scheme was utilized to enrich data sets for cross-linked peptides. This open-modification search based pipeline was shown to be useful for characterizing both chemical as well as native cross-links in proteins. The pipeline was validated by characterizing the known interactions in the chemically cross-linked CYP2E1--b5 complex. Utility of this method in identifying native cross-links was demonstrated by mapping disulfide bridges in RcsF, an outer membrane lipoprotein involved in Rcs phosphorelay.

Published
2008

24. A Molecular Scanner To Automate Proteomic Research and To Display Proteome Images

Author

Binz, Pierre-Alain, Muller, Markus, Walther, Daniel, Bienvenut, Willy V., Gras, Robin, Hoogland, Christine, Bouchet, Gerard, Gasteiger, Elisabeth, Fabbretti, Roberto, Gay, Steven, Palagi, Patricia, Wilkins, Marc R., Rouge, Veronique, Tonella, Luisa, Paesano, Salvo, Rossellat, Gerald, Karmime, Abderrahim, Bairoch, Amos, Sanchez, Jean-Charles, Appel, Ron D., and Hochstrasser, Denis F.

Subjects
Genomes -- Analysis, Molecular spectra -- Analysis, Scanning devices -- Design and construction, Proteins -- Research, Imaging systems -- Usage, Chemistry
Abstract

Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today's commonly used high-throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, a number of limitations stir adversely affect the rate of protein identification and annotation in 2-DE databases: the sequential excision process of pieces of gel containing protein; the enzymatic digestion step; the interpretation of mass spectra (reliability of identifications); and the manual updating of 2-DE databases. We present a highly automated method that generates a fully annotated 2-DE map. Using a parallel process, all proteins of a 2-DE are first simultaneously digested proteolytically and electro-transferred onto a poly(vinylidene difluoride) membrane. The membrane is then directly scanned by MALDI-TOF MS. After automated protein identification from the obtained peptide mass fingerprints using PeptIdent software (http://www. expasy, ch/tools/peptident, html), a fully annotated 2-D map is created on-line. It is a multidimensional representation of a proteome that contains interpreted PMF data in addition to protein identification results. This 'MS-imaging' method represents a major step toward the development of a clinical molecular scanner.

Published
1999

33. Labeling of Bifidobacterium longum cells with [super 13]C-substituted leucine for quantitative proteomic analyses

Author

Coute, Yohann, Hernandez, Celine, Appel, Ron D., Sanchez, Jean-Charles, and Margolles, Abelardo

Subjects
Bifidobacterium -- Physiological aspects, Leucine -- Analysis, Proteolysis -- Analysis, Biological sciences
Abstract

A quantitative proteomic strategy for the stable isotope labeling of Bifidobacterium longum cells with [super 13]C-substituted leucine is developed. The approach can be widely used for proteins with large number of variations.

Published
2007

34. The 1999 SWISS-2DPAGE database update

Author

Hoogland, Christine, Sanchez, Jean-Charles, Tonella, Luisa, Binz, Pierre-Alain, Bairoch, Amos, Hochstrasser, Denis F., Appel, Ron D., Hoogland, Christine, Sanchez, Jean-Charles, Tonella, Luisa, Binz, Pierre-Alain, Bairoch, Amos, Hochstrasser, Denis F., and Appel, Ron D.

Abstract

SWISS-2DPAGE (http://www.expasy.ch/ch2d/ ) is an annotated two-dimensional polyacrylamide gel electro­phoresis (2-DE) database established in 1993. The current release contains 24 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps have now 2824 identified spots, corresponding to 614 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence or any user-entered amino acids sequence. Last year improvements in the SWISS-2DPAGE database are as follows: three new maps have been created and several others have been updated; cross-references to newly built federated 2-DE databases have been added; new functions to access the data have been provided through the ExPASy proteomics server

Published
2017

35. Current status of the SWISS-2DPAGE database

Author

Hoogland, Christine, Sanchez, Jean-Charles, Tonella, Luisa, Bairoch, Amos, Hochstrasser, Denis F., Appel, Ron D., Hoogland, Christine, Sanchez, Jean-Charles, Tonella, Luisa, Bairoch, Amos, Hochstrasser, Denis F., and Appel, Ron D.

Abstract

The SWISS-2DPAGE database (http://www.expasy.ch/ch2d/ch2d-top.html) consists of two-dimensional polyacrylamide gel electrophoresis images, as well as textual descriptions of the proteins that have been identified on them. The current release contains 15 reference maps from human biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps have 2088 identified spots, corresponding to 410 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence

Published
2017

36. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Author

Stockinger, Heinz, Altenhoff, Adrian M., Arnold, Konstantin, Bairoch, Amos, Bastian, Frederic, Bergmann, Sven, Bougueleret, Lydie, Bucher, Philipp, Delorenzi, Mauro, Lane, Lydie, Mercier, Philippe Le, Lisacek, Frédérique, Michielin, Olivier, Palagi, Patricia M., Rougemont, Jacques, Schwede, Torsten, Mering, Christian von, Nimwegen, Erik van, Walther, Daniel, Xenarios, Ioannis, Zavolan, Mihaela, Zdobnov, Evgeny M., Zoete, Vincent, Appel, Ron D., Stockinger, Heinz, Altenhoff, Adrian M., Arnold, Konstantin, Bairoch, Amos, Bastian, Frederic, Bergmann, Sven, Bougueleret, Lydie, Bucher, Philipp, Delorenzi, Mauro, Lane, Lydie, Mercier, Philippe Le, Lisacek, Frédérique, Michielin, Olivier, Palagi, Patricia M., Rougemont, Jacques, Schwede, Torsten, Mering, Christian von, Nimwegen, Erik van, Walther, Daniel, Xenarios, Ioannis, Zavolan, Mihaela, Zdobnov, Evgeny M., Zoete, Vincent, and Appel, Ron D.

Abstract

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years

Published
2017

37. The SWISS-2DPAGE Database of Two-Dimensional Polyacrylamide Gel Electrophoresis, Its Status in 1995

Author

Appel, Ron D., Sanchez, Jean-Charles, Bairoch, Amos, Golaz, Olivier, Ravier, Florence, Pasquali, Christian, Hughes, Graham J., Hochstrasser, Denis F., Appel, Ron D., Sanchez, Jean-Charles, Bairoch, Amos, Golaz, Olivier, Ravier, Florence, Pasquali, Christian, Hughes, Graham J., and Hochstrasser, Denis F.

Abstract

SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The current release contains 343 entries of human, yeast (Saccharomyces cerevisiae) and Escherichia coli origin, as well as virtual entries for each of the protein sequences in the SWISS-PROT database

Published
2017

38. swissPIT: a novel approach for pipelined analysis of mass spectrometry data

Author

Quandt, Andreas, Hernandez, Patricia, Masselot, Alexandre, Hernandez, Céline, Maffioletti, Sergio, Pautasso, Cesare, Appel, Ron D., Lisacek, Frederique, Quandt, Andreas, Hernandez, Patricia, Masselot, Alexandre, Hernandez, Céline, Maffioletti, Sergio, Pautasso, Cesare, Appel, Ron D., and Lisacek, Frederique

Abstract

The identification and characterization of peptides from tandem mass spectrometry (MS/MS) data represents a critical aspect of proteomics. Today, tandem MS analysis is often performed by only using a single identification program achieving identification rates between 10-50% (Elias and Gygi, 2007). Beside the development of new analysis tools, recent publications describe also the pipelining of different search programs to increase the identification rate (Hartler et al., 2007; Keller et al., 2005). The Swiss Protein Identification Toolbox (swissPIT) follows this approach, but goes a step further by providing the user an expandable multi-tool platform capable of executing workflows to analyze tandem MS-based data. One of the major problems in proteomics is the absent of standardized workflows to analyze the produced data. This includes the pre-processing part as well as the final identification of peptides and proteins. The main idea of swissPIT is not only the usage of different identification tool in parallel, but also the meaningful concatenation of different identification strategies at the same time. The swissPIT is open source software but we also provide a user-friendly web platform, which demonstrates the capabilities of our software and which is available at http://swisspit.cscs.ch upon request for account. Contact: andreas.quandt@isb-sib.ch

Published
2017

39. The SWISS-2DPAGE database: what has changed during the last year

Author

Hoogland, Christine, Sanchez, Jean-Charles, Tonella, Luisa, Bairoch, Amos, Hochstrasser, Denis F., Appel, Ron D., Hoogland, Christine, Sanchez, Jean-Charles, Tonella, Luisa, Bairoch, Amos, Hochstrasser, Denis F., and Appel, Ron D.

Abstract

Swiss-2DPAGE (http://www.expasy.ch/ch2d/) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. The current release contains 21 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps now have 2480 identified spots, corresponding to 528 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence. During the last year, the SWISS-2DPAGE has undergone major changes. Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding source

Published
2017

40. ExPASy: the proteomics server for in-depth protein knowledge and analysis

Author

Gasteiger, Elisabeth, Gattiker, Alexandre, Hoogland, Christine, Ivanyi, Ivan, Appel, Ron D., Bairoch, Amos, Gasteiger, Elisabeth, Gattiker, Alexandre, Hoogland, Christine, Ivanyi, Ivan, Appel, Ron D., and Bairoch, Amos

Abstract

The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community

Published
2017

41. Accessing Reliable Health Information on the Web: A Review of the HON Approach.

Author

Boyer, Célia, Gaudinat, Arnaud, Hanbury, Allan, Appel, Ron D., Ball, Marion J., Carpentier, Michel, van Bemmel, Jan H., Bergmans, Jean-Paul, Hochstrasser, Denis, Lindber, Donald, Miller, Randolph, Peterschmitt, Jean-Claude, Safran, Charles, Thonnet, Michèle, and Geissbühler, Antoine

Subjects
MEDICAL informatics, HEALTH information services, MANAGEMENT of electronic health records, MEDICAL coding, WEB browsing, STANDARDS, SECURITY systems
Abstract

Accessing online health content of high quality and reliability presents challenges. Laypersons cannot easily differentiate trustworthy content from misinformed or manipulated content. This article describes complementary approaches for members of the general public and health professionals to find trustworthy content with as little bias as possible. These include the Khresmoi health search engine (K4E), the Health On the Net Code of Conduct (HONcode) and health trust indicator Web browser extensions. [ABSTRACT FROM AUTHOR]

Published
2017
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46. Proteome Imaging

Author

Palagi, Patricia M., primary, Walther, Daniel, additional, Zimmermann-Ivol, Catherine G., additional, and Appel, Ron D., additional

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