Quantify this! Report on a round table discussion on quantitative mass spectrometry in proteomics

Following the success of the first round table in 2001, the Swiss Proteomic Society has organized two additional specific events during its last two meetings: a proteomic application exercise in 2002 and a round table in 2003. Such events have as their main objective to bring together, around a challenging topic in mass spectrometry, two groups of specialists, those who develop and commercialize mass spectrometry equipment and software, and expert MS users for peptidomics and proteomics studies. The first round table (Geneva, 2001) entitled "Challenges in Mass Spectrometry" was supported by brief oral presentations that stressed critical questions in the field of MS development or applications (St?cklin and Binz, Proteomics 2002, 2, 825-827). Topics such as (i) direct analysis of complex biological samples, (ii) status and perspectives for MS investigations of noncovalent peptide-ligant interactions; (iii) is it more appropriate to have complementary instruments rather than a universal equipment, (iv) standardization and improvement of the MS signals for protein identification, (v) what would be the new generation of equipment and finally (vi) how to keep hardware and software adapted to MS up-to-date and accessible to all. For the SPS'02 meeting (Lausanne, 2002), a full session alternative event "Proteomic Application Exercise" was proposed. Two different samples were prepared and sent to the different participants: 100 micro g of snake venom (a complex mixture of peptides and proteins) and 10-20 micro g of almost pure recombinant polypeptide derived from the shrimp Penaeus vannamei carrying an heterogeneous post-translational modification (PTM). Among the 15 participants that received the samples blind, eight returned results and most of them were asked to present their results emphasizing the strategy, the manpower and the instrumentation used during the congress (Binz et. al., Proteomics 2003, 3, 1562-1566). It appeared that for the snake venom extract, the quality of the results was not particularly dependant on the strategy used, as all approaches allowed Lication of identification of a certain number of protein families. The genus of the snake was identified in most cases, but the species was ambiguous. Surprisingly, the precise identification of the recombinant almost pure polypeptides appeared to be much more complicated than expected as only one group reported the full sequence. Finally the SPS'03 meeting reported here included a round table on the difficult and challenging task of "Quantification by Mass Spectrometry", a discussion sustained by four selected oral presentations on the use of stable isotopes, electrospray ionization versus matrix-assisted laser desorption/ionization approaches to quantify peptides and proteins in biological fluids, the handling of differential two-dimensional liquid chromatography tandem mass spectrometry data resulting from high throughput experiments, and the quantitative analysis of PTMs. During these three events at the SPS meetings, the impressive quality and quantity of exchanges between the developers and providers of mass spectrometry equipment and software, expert users and the audience, were a key element for the success of these fruitful events and will have definitively paved the way for future round tables and challenging exercises at SPS meetings.     

Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session

After the success of the mass spectrometry (MS) round table that was held at the first Swiss Proteomics Society congress (SPS'01) in Geneva, the SPS has organized a proteomics application exercise and allocated a full session at the SPS'02 congress. The main objective was to encourage the exchange of expertise in protein identification, with a focus on the use of mass spectrometry, and to create a bridge between the users' questions and the instrument providers' solutions. Two samples were sent to fifteen interested labs, including academic groups and MS hardware providers. Participants were asked to identify and partially characterize the samples. They consisted of a complex mixture of peptide/proteins (sample A) and an almost pure recombinant peptide carrying post-translational modifications (sample B). Sample A was an extract of snake venom from the species Bothrops jararaca. Sample B was a recombinant and modified peptide derived from the shrimp Penaeus vannamei penaeidin 3a. The eight labs that returned results reported the use of a wide range of MS instrumentation and techniques. They mentioned a variety of time and manpower allocations. The origin of sample A was generally identified together with a number of database protein entries. The difficulty of the sample identification lay in the incomplete knowledge of the Bothrops species genome sequence and is discussed. Sample B was generally and correctly identified as penaeidin. However, only one group reported the full primary structure. Interestingly, the approaches were again varied and are discussed in the text.     

ISBP: Understanding the Security Rule of Users' Information-Sharing Behaviors in Partnership

The rapid growth of social network data has given rise to high security awareness among users, especially when they exchange and share their personal information. However, because users have different feelings about sharing their information, they are often puzzled about who their partners for exchanging information can be and what information they can share. Is it possible to assist users in forming a partnership network in which they can exchange and share information with little worry? We propose a modified information sharing behavior prediction (ISBP) model that can help in understanding the underlying rules by which users share their information with partners in light of three common aspects: what types of items users are likely to share, what characteristics of users make them likely to share information, and what features of users’ sharing behavior are easy to predict. This model is applied with machine learning techniques in WEKA to predict users’ decisions pertaining to information sharing behavior and form them into trustable partnership networks by learning their features. In the experiment section, by using two real-life datasets consisting of citizens’ sharing behavior, we identify the effect of highly sensitive requests on sharing behavior adjacent to individual variables: the younger participants’ partners are more difficult to predict than those of the older participants, whereas the partners of people who are not computer majors are easier to predict than those of people who are computer majors. Based on these findings, we believe that it is necessary and feasible to offer users personalized suggestions on information sharing decisions, and this is pioneering work that could benefit college researchers focusing on user-centric strategies and website owners who want to collect more user information without raising their privacy awareness or losing their trustworthiness.     

Advances in mass spectrometry-based cancer research and analysis: from cancer proteomics to clinical diagnostics

Introduction: The last 20 years have seen significant improvements in the analytical capabilities of biological mass spectrometry (MS). Studies using advanced MS have resulted in new insights into cell biology and the etiology of diseases as well as its use in clinical applications.

Areas covered: This review discusses recent developments in MS-based technologies and their cancer-related applications with a focus on proteomics. It also discusses the issues around translating the research findings to the clinic and provides an outline of where the field is moving.

Expert commentary: Proteomics has been problematic to adapt for the clinical setting. However, MS-based techniques continue to demonstrate potential in novel clinical uses beyond classical cancer proteomics.     

jmzTab: A Java interface to the mzTab data standard

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab‐delimited file that can capture identification and quantification results coming from MS‐based proteomics and metabolomics approaches. We here present an open‐source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table‐based sections in the mzTab files. In this article, as two example implementations, we also describe two stand‐alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com .     

Proteomic signatures of neuroinflammation in Alzheimer’s disease,multiple sclerosis and ischemic stroke

Introduction: Inflammation is integral in the neuropathology of both chronic and acute neurological disorders. Knowing the inflammatory profile is important for clarification of disease mechanisms, diagnostic purposes, and ultimately treatment options.

Areas covered: A systematic review was performed on literature from PubMed using the search terms ‘Alzheimer’s disease’ (AD) or ”multiple sclerosis” (MS) or ”ischemic stroke” and ‘proteomics’. Inflammatory proteins were assessed in blood, cerebrospinal fluid (CSF), and post-mortem brain tissue. Regulated inflammatory proteins across compartments and disorders mainly consisted of innate immune proteins, acute phase proteins and oxidative stress response proteins. In addition, immunoglobulin chains were signature proteins of MS, reflecting additional involvement of adaptive immunity. The Chitinase 3-like protein 1 was increased in ten original articles on MS and in three on AD supporting its implication in these diseases. Furthermore, CNS/CSF AD inflammatory proteins were matched to a CNS myeloid cell proteome implicating Alpha-2-Macroglobulin and Annexin A1 in AD pathogenesis.

Expert opinion: Proteomics is an excellent technique for profiling inflammatory proteins in tissues and cells, but still targeted approaches are required for profiling of very low abundance proteins and peptides. Knowing the inflammatory signature of brain tissue, CSF, blood, and CNS myeloid cells holds the potential to point to novel mechanistic aspects of neurological diseases.     

Report of the roundtable discussion organised by the Swiss Proteomics Society (SPS), Bern, 8th December 2004

How close are we to using proteomics tools in the every day practice of physicians? What are the socio-economical issues our health care system may face with the advent of biomarkers for early diagnosis? How to get the specialists from the various disciplines integrated in proteomics to establish a common understanding of the clinical issues and develop the necessary standards (methods, biochemicals and IT)? These were the kind of questions a panel of specialists tried to answer during the roundtable discussion that took place in Bern during the Swiss Proteomics Society 2004 congress.     

Occurrence of priapism after transient right MCAO in Swiss albino mice

Introduction: There are few reports about sexual problems in animal models after stroke. The aim of this paper is to report the occurrence of priapism after right MCAO in Swiss albino mice. In addition, we compared neurological score and apoptosis between the priapism-affected and unaffected mice.

Methods: Swiss albino mice were subjected to 45?min’ MCAO and 7?days’ reperfusion. Mice were observed before MCAO, then daily for 7?days to assess priapism. Neurological status and apoptosis (TUNEL assay) were assessed and compared in priapism and non-priapism mice.

Results: The results showed that the incidence of priapism after MCAO in Swiss albino mice were 65%. Priapism was detectable often at day 2 after stroke. Priapism-affected group had more severe behavioural deficits after stroke compared to non-priapism stroke mice.

Conclusion: Priapism after right MCAO is not rare in albino mice and could be considered as a marker of stroke severity. Further studies are needed to assess the incidence of priapism after stroke in other animal species used for stroke studies such as rat.     

Platelet proteomics: from discovery to diagnosis

Introduction: Platelets are the smallest cells within the circulating blood with key roles in physiological hemostasis and pathological thrombosis regulated by the onset of activating/inhibiting processes via receptor responses and signaling cascades.

Areas covered: Proteomics as well as genomic approaches have been fundamental in identifying and quantifying potential targets for future diagnostic strategies in the prevention of bleeding and thrombosis, and uncovering the complexity of platelet functions in health and disease. In this article, we provide a critical overview on current functional tests used in diagnostics and the future perspectives for platelet proteomics in clinical applications.

Expert commentary: Proteomics represents a valuable tool for the identification of patients with diverse platelet associated defects. In-depth validation of identified biomarkers, e.g. receptors, signaling proteins, post-translational modifications, in large cohorts is decisive for translation into routine clinical diagnostics.     

Assisted Suicide in Switzerland: Clarifying Liberties and Claims

Assisting suicide is legal in Switzerland if it is offered without selfish motive to a person with decision‐making capacity. Although the ‘Swiss model’ for suicide assistance has been extensively described in the literature, the formally and informally protected liberties and claims of assistors and recipients of suicide assistance in Switzerland are incompletely captured in the literature. In this article, we describe the package of rights involved in the ‘Swiss model’ using the framework of Hohfeldian rights as modified by Wenar. After outlining this framework, we dissect the rights involved in suicide assistance in Switzerland, and compare it with the situation in England and Germany. Based on this approach, we conclude that in Switzerland, claim rights exist for those requesting suicide assistance, and for those who are considering providing such assistance, even though no entitlements exist toward suicide assistance. We then describe the implementation of the ‘Swiss model’ and difficulties arising within it. Clarifying these issues is important to understand the Swiss situation, to evaluate what features of it may or may not be worth correcting or emulating, and to understand how it can impact requests for suicide assistance in other countries due to ‘suicide tourism’. It is also important to understand exactly what sets Switzerland apart from other countries with different legislations regarding suicide assistance.     

Only connect

Despite the fact that it has been said that the only people interested in definitions are those who wish to criticize them, I thank the five commentators. It has also been said that “the Linnean Society has been the medium for the publication of classical Memoirs upon Mimicry” (Poulton, 1898). I hope History will continue to be generous in its judgment on this latest round.     

Only connect

Despite the fact that it has been said that the only people interested in definitions are those who wish to criticize them, I thank the five commentators. It has also been said that "the Linnean Society has been the medium for the publication of classical Memoirs upon Mimicry" (Poulton, 1898). I hope History will continue to be generous in its judgment on this latest round.     

The potential impact of recent insights into proteomic changes associated with glaucoma

Introduction: Glaucoma, a major ocular neuropathy, is still far from being understood on a molecular scale. Proteomic workflows revealed glaucoma associated alterations in different eye components. By using state-of-the-art mass spectrometric (MS) based discovery approaches large proteome datasets providing important information about glaucoma related proteins and pathways could be generated. Corresponding proteomic information could be retrieved from various ocular sample species derived from glaucoma experimental models or from original human material (e.g. optic nerve head or aqueous humor). However, particular eye tissues with the potential for understanding the disease’s molecular pathomechanism remains underrepresented.

Areas covered: The present review provides an overview of the analysis depth achieved for the glaucomatous eye proteome. With respect to different eye regions and biofluids, proteomics related literature was found using PubMed, Scholar and UniProtKB. Thereby, the review explores the potential of clinical proteomics for glaucoma research.

Expert commentary: Proteomics will provide important contributions to understanding the molecular processes associated with glaucoma. Sensitive discovery and targeted MS approaches will assist understanding of the molecular interplay of different eye components and biofluids in glaucoma. Proteomic results will drive the comprehension of glaucoma, allowing a more stringent disease hypothesis within the coming years.     

Broadcasting in the airways: the fifth anniversary of the Radiation Research Podcast (1)

The Radiation Research Podcast was funded just over five years ago by a few Radiation Research Society members. To date, the volunteers running the podcast have produced and published online, open access, over 70 audio interviews. The program includes monthly interviews with authors of articles, award winners, and other recordings at conferences, such as round table discussions. We here present an overview of the podcast, from its creation to its fifth birthday, to explain how it is working, how the featured interviews are scheduled, and what future directions are taken. So, stay tuned!     

Human proteoforms as new targets for clinical mass spectrometry protein tests

Introduction: Only about dozen mass spectrometry (MS) protein tests have been translated into clinical laboratories since the MALDI and ESI approaches were developed thirty years ago. While the cost and complexity of these assays are important factors impeding their clinical adoption, new content generated via proteoforms detection could provide the impetus for further development and translation.

Areas covered: Provided here are several examples of MS-based protein assays capable of detecting proteoforms, including those for B-type natriuretic peptide (BNP) and parathyroid hormone (PTH). The evidence suggests that the ability to detect proteoforms is not enough to drive the clinical adoption of the MS-based tests – clinical utility of those proteoforms needs to be demonstrated first. Along those lines, recent efforts to discover, clinically validate, and initiate translation of novel proteoform biomarkers such as those of apolipoprotein C-III will be discussed.

Expert commentary: MS protein tests face a challenging future. Both the sample preparation steps and the MS platforms need to be simplified to bring the cost per test down, and then the new content brought by the detection of proteoforms will drive the proliferation of these MS tests – first in clinical utility studies and then for routine diagnostics.     

Quality meets quantity - quality control, data standards and repositories

In recent years, standardization and quality control have become important key points in industry, e.g. in drug discovery and for developing medical products. Is quality control in academic Proteomics a minor problem nowadays, where standard data formats and public repositories for data sharing exist? In this article, it is discussed how standard formats and repositories already support the documentation of quality control criteria in protein identification and quantification, and what has to be improved in the future: It is stated that the Proteomics community (represented by a group like the Proteomics Standards Initiative) will have to define a minimum document regarding quality control and to extend existing standards with additional quality control criteria enabling a substantial and standardized quality control process.     

The CCN family of genes: a perspective on CCN biology and therapeutic potential

The CCN family of genes currently comprises six secreted proteins (designated CCN1-6 after Cyr61/CCN1; ctgf/CCN2; Nov/CCN3; WISP1/CCN4; WISP2/CCN5, WISP3/CCN6) with a similar mosaic primary structure. It is now well accepted that CCN proteins are not growth factors but matricellular proteins that modify signaling of other molecules, in particular those associated with the extracellular matrix. CCN proteins are involved in mitosis, adhesion, apoptosis, extracellular matrix production, growth arrest and migration of multiple cell types. Since their first identification as matricellular factors, the CCN proteins now figure prominently in a variety of major diseases and are now considered valid candidates for therapeutic targeting. Dissection of the molecular mechanisms governing the biological properties of these proteins is being actively pursued by an expanding network of scientists around the globe who will meet this year at the 5th International Workshop on the CCN family of Genes, organized by the International CCN Society ( http://ccnsociety.com ), home for an international cadre of collaborators working in the CCN field.     

The jmzQuantML programming interface and validator for the mzQuantML data standard

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools ( http://code.google.com/p/jmzquantml/ ). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool ( http://code.google.com/p/mzquantml‐validator/ ) for validating mzQuantML files, which is a formal part of the data standard.     

Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow

The European Proteomics Association (EuPA) 2012 Scientific Congress ‘New Horizons and Applications for Proteomics’, hosted by the British Society for Proteome Research (BSPR)

Glasgow, Scotland, UK, 12 July 2012

Cross-linking/mass spectrometry ended decades of method developments and entered the era of applications at this year’s European Proteomics Association meeting. The train has started moving, with successful applications of this tool by multiple pioneering laboratories addressing biological and structural problems. Proteomics, on the other side, sees ever increasing data volumes, leading to questions as to how to store the data mountain publically, use it and convert it into testable hypotheses. The European Proteomics Association meeting has been complementary to the American Society for Mass Spectrometry meeting in many ways, also thanks to its more manageable size and the vision of the organizers in inviting some of Europe’s best emerging minds.