DATASET BRIEF Yeast proteome map (update 2006) Michel Perrot 1 , Anne-Laure Guieysse-Peugeot 1 * , Aurélie Massoni 1 , Christelle Espagne 1 ** , Stéphane Claverol 2 , Raquel Monteiro Silva 3 , Paul Jenö 4 , Manuel Santos 3 , Marc Bonneu 2 and Hélian Boucherie 1 1 Institut de Biochemie et Génétique Cellulaires, UMR CNRS 5095, Bordeaux, France 2 Pôle Protéomique, Plateforme Génomique Fonctionnelle Bordeaux, Université Victor Segalen Bordeaux 2, Bordeaux, France 3 Deparmento de Biologia, Universidade de Aveiro, Aveiro, Portugal 4 Department of Biochemistry, Biozentrum of the University of Basel, Basel, Switzerland To improve the potential of two-dimensional gel electrophoresis for proteomic investigations in yeast we have undertaken the systematic identification of Saccharomyces cerevisiae proteins sepa- rated on 2-D gels. We report here the identification of 187 novel protein spots. They were identi- fied by two methods, mass spectrometry and gene inactivation. These identifications extend the number of protein spots identified on our yeast 2-D proteome map to 602, i.e. nearly half the detectable spots of the proteome map. These spots correspond to 417 different proteins. The reference map and the list of identified proteins can be accessed on the Yeast Protein Map server (www.ibgc.u-bordeaux2.fr/YPM). Received: August 28, 2006 Revised: November 30, 2006 Accepted: January 3, 2006 Keywords: Proteome / Saccharomyces cerevisiae / Yeast Proteomics 2007, 7, 1117–1120 1117 A great deal of effort has been spent into the mapping of proteins of model organisms such as Saccharomyces cerevisiae by 2-DE. The first annotated yeast map was reported by McLaughlin’s group in 1982 [1]. This map contained 21 identified spots. Since this pioneering work, several well- documented yeast reference maps have been established. They correspond to proteins from total cellular extracts [2–7], strongly alkaline [8] or mitochondrial proteins [9, 10]. The number of protein spots identified in these studies ranges from 150 to 460. These annotated maps have proved to be useful for the investigation of a wide variety of biological problems (for a review see Ref. [11]). Although the number of proteins presently identified on the yeast reference maps is already significant, a large num- ber of protein spots remains to be identified in order to take full advantage of the separation power of 2-DE. In our labo- ratory, previous investigations allowed us to establish a reference map of yeast proteins from total cellular extracts in the pH range of 4 to 7 [5]. Four hundred and fifteen spots were identified on this map. To improve our view of the yeast proteome we sought to identify novel spots by using MS and gene inactivation. The spot identifications were carried out using two types of gels. One corresponds to previously used gels while the other reveals an extended reference map. Figure 1 shows the 2-D pattern of the standard reference map. It corresponds to the soluble proteins synthesized by strain S288C exponen- tially growing on a glucose containing synthetic medium. The first dimension ranges from pH 4.2 to 6.8 and the sec- ond dimension from 15 to 200 kDa. The pattern contains 1200 spots. The extended reference map is shown in Fig. 2. The first dimension ranges from pH 3.5 to 7.0 and the sec- ond dimension from 13.5 to 200 kDa. In comparison with the standard 2-D pattern, 150 additional proteins are found on this gel. Correspondence: Dr. Hélian Boucherie, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, F-33077 Bordeaux, France E-mail: H.Boucherie@ibgc.u-bordeaux2.fr Fax: 133-5-5699-9068 * Current address: INSERM U565, UMR CNRS 5153, Museum National d’Histoire Naturelle, Paris, France ** Current address: ISV, CNRS, Gif-sur-Yvette, France DOI 10.1002/pmic.200600952  2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com