Juan-Pablo Albar

Incomplete tyrosine 1680 sulphation in recombinant FVIII concentrates

condition of obligate carrier of haemophilia A. When we performed the test with usual combinations of oligonucleotides, 9Fint1h-2F -9cR (reaction 1) and 9Fint1h-2F int1h-2R (reaction 2) for analysis of family members, we found that the proband s mother and daughter were carriers of the same genetic pattern as the proband while the proband s sister did not show Inv1 (Fig. 1). To our knowledge, this is the first report describing this aberrant band pattern. Sukarova et al. reported two cases with an abnormal Inv1 pattern in Macedônia which, however, was different from the one reported here [5]. Preliminary experiments suggest that the defect reported here is due to the presence of an extra int1h copy, mediating the recombination event. In conclusion, we present the case of a patient with severe HA with an aberrant pattern of Inv1 not reported to date. This case confirms the importance of detecting the Inv1 and illustrates the complex molecular mechanisms associated with HA.

Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 8th Annual HUPO World Congress updated the delegates on the current status of the ongoing work of this group. The mass spectrometry group reviewed the progress of mzML since its release last year and detailed new work on providing a common format for SRM/MRM transition lists (TraML). The implementation of mzIdentML, for describing the output of proteomics search engines, was outlined and the release of a new web service PSICQUIC, which allows users to simultaneously search multiple interaction databases, was announced. Finally, the audience participated in a lively debate, discussing both the benefits of these standard formats and issues with their adoption and use in a research environment.

Relevance of proteomics standards for the ProteoRed Spanish organization

ProteoRed, a Spanish Initiative in the field of proteomics, is reaching international standards. Here we present ProteoRed as an example of collaborative initiative in the field of proteomics. Being established as a high level proteomics service provider, it also has consolidated as one of the first institutions really involved in implementing proteomics standards developed by the HUPO consortium. As a collaborative network it has proved a valuable platform to coordinate multi-centric experiments aiming at evaluating the robustness of laboratory workflows as well as the implementation of standards. In addition, this initiative has been very active in promoting the interaction between clinicians and basic researchers by means of courses, workshops or symposia like the one highlighted in this report, which was devoted to clinical proteomics and took place in La Coruña, Spain, last September.

Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO‐PSI 28–30 March 2010, Seoul, South Korea

The annual Spring Workshop of the HUPO‐PSI took place in Korea, where the Mass Spectrometry and Protein Separations groups joined forces to tackle the issue of the consistent reporting of quantitative proteomic data generated by mass‐spectrometry‐based technologies. A preliminary mzQuantML schema was drafted which, when completed and tested, will complement the existing mzIdentML schema for reporting protein identifications. The Molecular Interactions group concentrated on the implementations of the PSICQUIC (PSI Common Query InterfaCe) service that allows users to simultaneously query interaction data across multiple participating resources. Work was also undertaken to update the MIAPE guidelines, in response to feedback from the editors of a number of proteomic journals.

Annual Spring Meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain

The role of the Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) is to produce and release community‐accepted reporting requirements, interchange formats and controlled vocabularies for mass spectrometry proteomics and related technologies such as gel electrophoresis, column chromatography and molecular interactions. A number of significant advances were made at this workshop, with the new MS standard, mzML, being finalised prior to release on 1st June 2008 and analysisXML, which will allow protein and peptide identifications and post‐translational modifications to be captured, being prepared to enter the review process this summer. The accompanying controlled vocabularies are continuing to evolve and a number of standards papers are now being finalised prior to publication.

From proteomics data representation to public data flow: A report on the HUPO-PSI workshop september 2011, Geneva, Switzerland

The plenary session of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization at the Tenth annual HUPO World Congress updated the delegates on the ongoing activities of this group. The Molecular Interactions workgroup described the success of the PSICQUIC web service, which enables users to access multiple interaction resources with a single query. One user instance is the IMEx Consortium, which uses the service to enable users to access a non‐redundant set of protein–protein interaction records. The mass spectrometry data formats, mzML for mass spectrometer output files and mzIdentML for the output of search engines, are now successfully established with increasing numbers of implementations. A format for the output of quantitative proteomics data, mzQuantML, and also TraML, for SRM/MRM transition lists, are both currently nearing completion. The corresponding MIAPE documents are being updated in line with advances in the field, as is the shared controlled vocabulary PSI‐MS. In addition, the mzTab format was introduced, as a simpler way to report MS proteomics and metabolomics results. Finally, the ProteomeXchange Consortium, which will supply a single entry point for the submission of MS proteomics data to multiple data resources including PRIDE and PeptideAtlas, is currently being established.

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.

The Annual Spring workshop of the HUPO‐PSI was this year held at the EMBL International Centre for Advanced Training (EICAT) in Heidelberg, Germany. Delegates briefly reviewed the successes of the group to date. These include the wide spread implementation of the molecular interaction data exchange formats, PSI‐MI XML2.5 and MITAB, and also of mzML, the standard output format for mass spectrometer output data. These successes have resulted in enhanced accessibility to published data, for example the development of the PSICQUIC common query interface for interaction data and the development of databases such as PRIDE to act as public repositories for proteomics data and increased biosharing, through the development of consortia, for example IMEx and ProteomeXchange which will both share the burden of curating the increasing amounts of data being published and work together to make this more accessible to the bench scientist. Work then started over the three days of the workshop, with a focus on advancing the draft format for handling quantitative mass spectrometry data (mzQuantML) and further developing TraML, a standardized format for the exchange and transmission of transition lists for SRM experiments.

Inverse regulation in the metabolic genes pckA and metE revealed by proteomic analysis of the Salmonella RcsCDB regulon.

The RcsC, RcsD, and RcsB proteins compose a system used by enteric bacteria to sense envelope stress. Signal transmission occurs from the sensor RcsC to the transcriptional regulator RcsB. Accessory proteins, such as IgaA, are known to adjust the response level. In a previous transcriptomic study, we uncovered 85 genes differentially expressed in Salmonella enterica serovar Typhimurium igaA mutants. Here, we extended these observations to proteomics by performing differential isotope-coded protein labeling (ICPL) followed by liquid chromatography-electrospray ionization tandem mass spectrometry. Five-hundred five proteins were identified and quantified, with 75 of them displaying significant changes in response to alterations in the RcsCDB system. Divergent expression at the RNA and protein level was observed for the metabolic genes pckA and metE, involved in gluconeogenesis and methionine synthesis, respectively. When analyzed in diverse environmental conditions, including the intracellular niche of eukaryotic cells, inverse regulation was more evident for metE and in bacteria growing in defined minimal medium or to stationary phase. The RcsCDB system was also shown to repress the synthesis of the small RNA FnrS, previously reported to modulate metE expression. Collectively, these findings provide new insights into post-transcriptional regulatory mechanisms involving the RcsCDB system and its control over metabolic functions.

EuPA achieves visibility – an activity report on the first three years

Plans for the European Proteomics Association (EuPA) were conceived and established during 2004 and 2005, and culminated in the formal inception of the organisation during the 4th HUPO World Congress held in Munich in 2005. The mission from the outset has been three-tiered and is to: i) strengthen the national Proteomics organizations in their efforts; ii) to co-ordinate and provide educational programs, and iii) to advance the networking of scientists through meetings, workshops and student exchange. Linked to the mission were objectives to emphasise the benefits and contributions of Proteomics to biological and industrial researchers, the general public and science policy makers in Europe. In addition, the EuPA set out to promote scientific exchange for all applications and technology development related to Proteomics, and coordinate joint activities of national Proteomics societies at the European level. To achieve these tasks an organisational structure was conceived whereby four Activity Committees (Conferences/Communications, Education, EuPA-HUPO-Interactions and Funding) were implemented and a General Council consisting of all member countries. The remarkable rise and progress the EuPA has achieved in this small time frame is reported here.