Johannes Griss

Johannes Griss
Medical University of Vienna | MedUni Vienna · Division of Immunology, Allergy and Infectious Skin Diseases

35.66
 · 
MD, Ph.D.

About

87
Publications
7,492
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Introduction
Johannes Griss currently works at the Division of Immunology, Allergy and Infectious Skin Diseases, Medical University of Vienna. Johannes research focuses on algorithms for MS/MS based proteomics data analysis (spectrum clustering) and the integration of multi-omics biomedical datasets.

Publications

Publications (87)
Preprint
Full-text available
Pathway analyses are key methods to analyse 'omics experiments. Nevertheless, integrating data from different 'omics technologies and different species still requires considerable bioinformatics knowledge. Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactom...
Article
Full-text available
Prostate cancer (PCa) has a broad spectrum of clinical behavior; hence, biomarkers are urgently needed for risk stratification. Here, we aim to find potential biomarkers for risk stratification, by utilizing a gene co-expression network of transcriptomics data in addition to laser-microdissected proteomics from human and murine prostate FFPE sample...
Preprint
Full-text available
Motivation: Spectrum clustering has been proved to enhance proteomics data analysis: some originally unidentified spectra can be potentially identified and individual peptides can also be evaluated to find potentially mis-identifications by using clusters of identified spectra. The Phoenix Enhancer spectrum service/tool provides an infrastructure t...
Preprint
Full-text available
Prostate cancer (PCa) has a broad spectrum of clinical behaviour, hence biomarkers are urgently needed for risk stratification. We previously described the protective effect of STAT3 in a prostate cancer mouse model. By utilizing a gene co-expression network in addition to laser microdissected proteomics from human and murine prostate FFPE samples,...
Article
Full-text available
Tumor associated inflammation predicts response to immune checkpoint blockade in human melanoma. Current theories on regulation of inflammation center on anti-tumor T cell responses. Here we show that tumor associated B cells are vital to melanoma associated inflammation. Human B cells express pro- and anti-inflammatory factors and differentiate in...
Article
The order of enzymatic activity across Golgi cisternae is essential for complex molecule biosynthesis. However, an inability to separate Golgi cisternae has meant that the cisternal distribution of most resident proteins, and their underlying localization mechanisms, are unknown. Here, we exploit differences in surface charge of intact cisternae to...
Article
Full-text available
Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) proteomics datasets. We show that spectral clustering can also be used to infer additional peptide-spectrum...
Article
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Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence a manuscript’s methods sec...
Preprint
Full-text available
Tumor associated inflammation is one of important predictors of response to immune checkpoint blockade. Understanding molecular processes that regulate tumor inflammation is key to improve the efficacy of checkpoint blockade. Established mechanisms that underlie therapy response and resistance have centered on anti-tumor T cell responses. We show t...
Article
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The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous...
Preprint
Full-text available
Mass spectrometry coupled with isobaric labelling provides fast large-scale comparison of protein abundances over multiple conditions. To date, no one-stop-shop software solution exists that enables non-bioinformatics experts to carry out the full analysis of the acquired raw data with minimal intervention. Mostly, pipelines for such analyses are b...
Article
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further...
Poster
Full-text available
Introduction There is an increasing demand for approaches to integrate proteomics data with other ‘omics’ data types, especially genomics. In fact, current resources to integrate proteomics in a genome context are insufficient for large-scale studies. To bring the genomics and proteomics results into coherence, novel resources must be developed th...
Article
In this Viewpoint article, we discuss current and future applications of spectral clustering in the context of mass spectrometry‐based proteomics approaches. First of all, we are introducing the main algorithms and tools that can currently be used to perform spectral clustering. In addition, we explain its main applications and their use in current...
Article
In the recent benchmarking article entitled “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”, Rieder et al. compared several different approaches to cluster MS/MS spectra. While we certainly recognize the value of the manuscript, here, we report some shortcomings detected in the original analyses. For most analyses, the...
Article
Aims Immune checkpoint inhibitors have become a successful treatment in metastatic melanoma. The high response rates in a subset of patients suggest that a sensitive companion diagnostic test is required. The predictive value of programmed death ligand 1 (PD‐L1) staining in melanoma has been questioned due to inconsistent correlation with clinical...
Article
Full-text available
In melanoma, therapies with inhibitors to oncogenic BRAFV600E are highly effective but responses are often short-lived due to the emergence of drug-resistant tumor subpopulations. We describe here a mechanism of acquired drug resistance through the tumor microenvironment, which is mediated by human tumor-associated B cells. Human melanoma cells con...
Article
Background: Intravascular large B-cell lymphoma (IVLBCL) is a rare type of extranodal large B-cell lymphoma. It is characterized by the proliferation of tumour cells exclusively intraluminally in small blood vessels of different organs. The clinical manifestation depends on the type of organ affected, additionally, a haemophagocytic syndrome can b...
Article
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Motivation: BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful ana...
Article
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The authors wish to correct the affiliation of one of the authors. GerhardMayer's only affiliation should be ³Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany. He does NOT have a second affiliation at: ¹European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Camp...
Article
Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average, 75% of spectra analyzed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large scale to shed light on these unidentified spectra. The Proteomics Identifications (PRIDE) Database Archive is one of the largest MS proteo...
Article
Full-text available
B cells often infiltrate the microenvironment of human tumors. B cells can both positively and negatively regulate anti-tumor immune responses. In several human cancers, higher numbers of CD20(+) tumor associated B cells (TAB) are associated with a favorable prognosis, whereas in human primary melanomas this association is contentious. In this stud...
Article
Full-text available
Chemically modified trypsin is a standard reagent in proteomics experiments but is usually not considered in database searches. Modification of trypsin is supposed to protect the protease against autolysis and the resulting loss of activity. Here we show that modified trypsin is still subject to self-digestion and as a result modified trypsin deriv...
Article
Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend expe...
Article
Full-text available
The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data...
Article
Full-text available
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources...
Article
Dermatitis herpetiformis (DH) is a highly pruritic, symmetric, papulo-vesicular dermatosis with lesions most predominantly found on the extensor surfaces of the extremities. It is currently the only dermatosis characterized by granular IgA deposits in the papillary dermis as visualized by direct immunofluorescence (IF) microscopy from perilesional...
Article
Full-text available
In this manuscript, we provide a comprehensive study of the content of UniProt protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt Knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding IPI (International Protein Index), RefSeq, Ensembl and UniRef100...
Article
Full-text available
Detecting serum-autoantibodies by anti-Desmoglein-1 (anti-Dsg1) and anti-Dsg3 ELISAs as well as indirect immunofluorescence (IIF) are established complementary methods to diagnose pemphigus. Whether autoantibody levels also reflect clinical disease activity is still a matter of debate, as head-to-head comparisons of ELISA values and IIF titres with...
Article
Full-text available
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics a...
Article
Full-text available
SRM: Selected Reaction MonitoringTargeted personalized treatment options have become a major hope of clinical (e.g. cancer) research within the past years [1]. Success stories like herceptin [2] in breast cancer and BRAFV600E inhibitors [3] in melanoma have kindled the quest to identify novel biomarkers for diagnosis, patient stratification and per...
Article
Full-text available
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics a...
Article
Full-text available
mzTab is the most recent standard format developed by the Proteomics Standards Initiative (PSI). mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from mass spectrometry (MS)-based proteomics and metabolomics approaches. We here present an open-source Java Application Programming Interface (API...
Article
Full-text available
Melanoma, the deadliest form of skin cancer, is highly immunogenic and frequently infiltrated with immune cells including B cells. The role of tumor-infiltrating B cells (TIBCs) in melanoma is as yet unresolved, possibly due to technical challenges in obtaining TIBCs in sufficient quantity for extensive studies and due to the limited life span of B...
Article
Drug resistance is a major obstacle in melanoma treatment. Recognition of specific resistance patterns, the understanding of the patho-physiology of drug resistance and identification of remaining options for individual melanoma treatment would greatly improve therapeutic success. We performed mass spectrometry-based proteome profiling of A375 mela...
Data
Full-text available
List of PRIDE XML files submitted to the PRIDE database.
Data
Full-text available
Proteins identified in untreated (con) and inflammatory activated (act) PBMCs by shotgun proteomics. Nine independent experiments out of six different donors for each group were pooled. The positive identification rates are listed for each protein for each group (pos-id; e.g. 3/9: three independent identifications out of nine experiments). Proteins...
Article
Full-text available
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content,...
Article
Full-text available
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implem...
Article
Full-text available
Proteome profiling is the method of choice to identify marker proteins whose expression may be characteristic for certain diseases. The formation of such marker proteins results from disease-related pathophysiologic processes. In healthy individuals, peripheral blood mononuclear cells (PBMCs) circulate in a quiescent cell state monitoring potential...
Article
Full-text available
We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, t...
Article
Full-text available
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software imp...
Article
Full-text available
The International Protein Index (IPI) database has been one of the most widely used protein databases in MS proteomics approaches. Recently, the closure of IPI in September 2011 was announced. Its recommended replacement is the new UniProt Knowledgebase (UniProtKB) "complete proteome" sets, launched in May 2011. Here, we analyze the consequences of...