20 Search Results for "Huber, Christian G."

Document
DOI: 10.4230/LIPIcs.COSIT.2024.7
What Is a Spatio-Temporal Model Good For?: Validity as a Function of Purpose and the Questions Answered by a Model

Authors: Simon Scheider and Judith A. Verstegen

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
The concept of validity is a cornerstone of science. Given this central role, it is somewhat surprising to find that validity remains a rather obscure concept. Unfortunately, the term is often reduced to a matter of ground truth data, seemingly because we fail to come to grips with it. In this paper, instead, we take a purpose-based approach to the validity of spatio-temporal models. We argue that a model application is valid only if the model delivers an answer to a particular spatio-temporal question specifying some experiment including spatio-temporal controls and measures. Such questions constitute the information purposes of models, forming an intermediate layer in a pragmatic knowledge pyramid with corresponding levels of validity. We introduce a corresponding question-based grammar that allows us to formally distinguish among contemporary inference, prediction, retrodiction, projection, and retrojection models. We apply the grammar to corresponding examples and discuss the possibilities for validating such models as a means to a given end.
Cite as

Simon Scheider and Judith A. Verstegen. What Is a Spatio-Temporal Model Good For?: Validity as a Function of Purpose and the Questions Answered by a Model. In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{scheider_et_al:LIPIcs.COSIT.2024.7,
  author =	{Scheider, Simon and Verstegen, Judith A.},
  title =	{{What Is a Spatio-Temporal Model Good For?: Validity as a Function of Purpose and the Questions Answered by a Model}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.7},
  URN =		{urn:nbn:de:0030-drops-208225},
  doi =		{10.4230/LIPIcs.COSIT.2024.7},
  annote =	{Keywords: validity, fitness-for-purpose, spatio-temporal modeling, pragmatics, question grammar}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.3
An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree

Authors: Yao-ban Chan

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The phylogenies of species and the genes they contain are similar but distinct, due to evolutionary events that affect genes but do not create new species. These events include gene duplication and loss, but also paralog exchange (non-allelic homologous recombination), where duplicate copies of a gene recombine. To account for paralog exchange, the evolutionary history of the genes must be represented in the form of a phylogenetic network. We reconstruct the interlinked evolution of the genes and species with reconciliations, which map the gene network into the species tree by explicitly accounting for these events. In previous work, we proposed the problem of reconciling a gene network and a species tree, but did not find an efficient solution for a general gene network. In this paper, we develop such a solution, and prove that it solves the most parsimonious reconciliation problem. Our algorithm is exponential only in the level of the gene network (with a base of 2), and we demonstrate that it is a practical solution through simulations. This allows, for the first time, a fine-grained study of the paralogy/orthology relationship between genes along their sequences.
Cite as

Yao-ban Chan. An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chan:LIPIcs.WABI.2024.3,
  author =	{Chan, Yao-ban},
  title =	{{An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{3:1--3:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.3},
  URN =		{urn:nbn:de:0030-drops-206472},
  doi =		{10.4230/LIPIcs.WABI.2024.3},
  annote =	{Keywords: Reconciliation, recombination, paralog exchange, phylogenetic network, gene duplication, gene loss}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2024.10
Second-Order Generalised Algebraic Theories: Signatures and First-Order Semantics

Authors: Ambrus Kaposi and Szumi Xie

Published in: LIPIcs, Volume 299, 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)

Abstract
Programming languages can be defined from the concrete to the abstract by abstract syntax trees, well-scoped syntax, well-typed (intrinsic) syntax, algebraic syntax (well-typed syntax quotiented by conversion). Another aspect is the representation of binding structure for which nominal approaches, De Bruijn indices/levels and higher order abstract syntax (HOAS) are available. In HOAS, binders are given by the function space of an internal language of presheaves. In this paper, we show how to combine the algebraic approach with the HOAS approach: following Uemura, we define languages as second-order generalised algebraic theories (SOGATs). Through a series of examples we show that non-substructural languages can be naturally defined as SOGATs. We give a formal definition of SOGAT signatures (using the syntax of a particular SOGAT) and define two translations from SOGAT signatures to GAT signatures (signatures for quotient inductive-inductive types), based on parallel and single substitutions, respectively.
Cite as

Ambrus Kaposi and Szumi Xie. Second-Order Generalised Algebraic Theories: Signatures and First-Order Semantics. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kaposi_et_al:LIPIcs.FSCD.2024.10,
  author =	{Kaposi, Ambrus and Xie, Szumi},
  title =	{{Second-Order Generalised Algebraic Theories: Signatures and First-Order Semantics}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-323-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{299},
  editor =	{Rehof, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2024.10},
  URN =		{urn:nbn:de:0030-drops-203396},
  doi =		{10.4230/LIPIcs.FSCD.2024.10},
  annote =	{Keywords: Type theory, universal algebra, inductive types, quotient inductive types, higher-order abstract syntax, logical framework}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2024.22
Automating Boundary Filling in Cubical Agda

Authors: Maximilian Doré, Evan Cavallo, and Anders Mörtberg

Published in: LIPIcs, Volume 299, 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)

Abstract
When working in a proof assistant, automation is key to discharging routine proof goals such as equations between algebraic expressions. Homotopy Type Theory allows the user to reason about higher structures, such as topological spaces, using higher inductive types (HITs) and univalence. Cubical Agda is an extension of Agda with computational support for HITs and univalence. A difficulty when working in Cubical Agda is dealing with the complex combinatorics of higher structures, an infinite-dimensional generalisation of equational reasoning. To solve these higher-dimensional equations consists in constructing cubes with specified boundaries. We develop a simplified cubical language in which we isolate and study two automation problems: contortion solving, where we attempt to "contort" a cube to fit a given boundary, and the more general Kan solving, where we search for solutions that involve pasting multiple cubes together. Both problems are difficult in the general case - Kan solving is even undecidable - so we focus on heuristics that perform well on practical examples. We provide a solver for the contortion problem using a reformulation of contortions in terms of poset maps, while we solve Kan problems using constraint satisfaction programming. We have implemented our algorithms in an experimental Haskell solver that can be used to automatically solve goals presented by Cubical Agda. We illustrate this with a case study establishing the Eckmann-Hilton theorem using our solver, as well as various benchmarks - providing the ground for further study of proof automation in cubical type theories.
Cite as

Maximilian Doré, Evan Cavallo, and Anders Mörtberg. Automating Boundary Filling in Cubical Agda. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dore_et_al:LIPIcs.FSCD.2024.22,
  author =	{Dor\'{e}, Maximilian and Cavallo, Evan and M\"{o}rtberg, Anders},
  title =	{{Automating Boundary Filling in Cubical Agda}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{22:1--22:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-323-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{299},
  editor =	{Rehof, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2024.22},
  URN =		{urn:nbn:de:0030-drops-203514},
  doi =		{10.4230/LIPIcs.FSCD.2024.22},
  annote =	{Keywords: Cubical Agda, Automated Reasoning, Constraint Satisfaction Programming}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2024.10
Crêpe: Clock-Reconfiguration-Aware Preemption Control in Real-Time Systems with Devices

Authors: Eva Dengler and Peter Wägemann

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)

Abstract
The domain of energy-constrained real-time systems that are operated on modern embedded system-on-chip (SoC) platforms brings numerous novel challenges for optimal resource minimization. These modern hardware platforms offer a heterogeneous variety of features to configure the tradeoff between temporal performance and energy efficiency, which goes beyond the state-of-the-art of existing dynamic-voltage-frequency-scaling (DVFS) scheduling schemes. The control center for configuring this tradeoff on platforms are complex clock subsystems that are intertwined with requirements of the SoC’s components (e.g., transceiver/memory/sensor devices). That is, several devices have precedence constraints with respect to specific clock sources and their settings. The challenge of dynamically adapting the various clock sources to select resource-optimal configurations becomes especially challenging in the presence of asynchronous preemptions, which are inherent to systems that use devices. In this paper, we present Crêpe, an approach to clock-reconfiguration-aware preemption control: Crêpe has an understanding of the target platform’s clock subsystem, its sleep states, and penalties to reconfigure clock sources for adapting clock frequencies. Crêpe’s hardware model is combined with an awareness of the application’s device requirements for each executed task, as well as possible interrupts that cause preemptions during runtime. Using these software/hardware constraints, Crêpe employs, in its offline phase, a mathematical formalization in order to select energy-minimal configurations while meeting given deadlines. This optimizing formalization, processed by standard mathematical solver tools, accounts for potentially occurring interrupts and the respective clock reconfigurations, which are then forwarded as alternative schedules to Crêpe’s runtime system. During runtime, the dispatcher assesses these offline-determined alternative schedules and reconfigures the clock sources for energy minimization. We developed an implementation based on a widely-used SoC platform (i.e., ESP32-C3) and an automated testbed for comprehensive energy-consumption evaluations to validate Crêpe’s claim of selecting resource-optimal settings under worst-case considerations.
Cite as

Eva Dengler and Peter Wägemann. Crêpe: Clock-Reconfiguration-Aware Preemption Control in Real-Time Systems with Devices. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 10:1-10:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dengler_et_al:LIPIcs.ECRTS.2024.10,
  author =	{Dengler, Eva and W\"{a}gemann, Peter},
  title =	{{Cr\^{e}pe: Clock-Reconfiguration-Aware Preemption Control in Real-Time Systems with Devices}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{10:1--10:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.10},
  URN =		{urn:nbn:de:0030-drops-203135},
  doi =		{10.4230/LIPIcs.ECRTS.2024.10},
  annote =	{Keywords: energy-constrained real-time systems, time/energy tradeoff, system-on-chip, energy-aware real-time scheduling, resource minimization, preemption control, worst-case energy consumption (WCEC), worst-case execution time (WCET), static whole-system analysis}
}
Document
DOI: 10.4230/DagSemProc.05471.3
A machine learning approach for prediction of DNA and peptide HPLC retention times

Authors: Marc Sturm, Sascha Quinten, Christian G. Huber, and Oliver Kohlbacher

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
High performance liquid chromatography (HPLC) has become one of the most efficient methods for the separation of biomolecules. It is an important tool in DNA purification after synthesis as well as DNA quantification. In both cases the separability of different oligonucleotides is essential. The prediction of oligonucleotide retention times prior to the experiment may detect superimposed nucleotides and thereby help to avoid futile experiments. In 2002 Gilar et al. proposed a simple mathematical model for the prediction of DNA retention times, that reliably works at high temperatures only (at least 70°C). To cover a wider temperature rang we incorporated DNA secondary structure information in addition to base composition and length. We used support vector regression (SVR) for the model generation and retention time prediction. A similar problem arises in shotgun proteomics. Here HPLC coupled to a mass spectrometer (MS) is used to analyze complex peptide mixtures (thousands of peptides). Predicting peptide retention times can be used to validate tandem-MS peptide identifications made by search engines like SEQUEST. Recently several methods including multiple linear regression and artificial neural networks were proposed, but SVR has not been used so far.
Cite as

Marc Sturm, Sascha Quinten, Christian G. Huber, and Oliver Kohlbacher. A machine learning approach for prediction of DNA and peptide HPLC retention times. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{sturm_et_al:DagSemProc.05471.3,
  author =	{Sturm, Marc and Quinten, Sascha and Huber, Christian G. and Kohlbacher, Oliver},
  title =	{{A machine learning approach for prediction of DNA and peptide HPLC retention times}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.3},
  URN =		{urn:nbn:de:0030-drops-5484},
  doi =		{10.4230/DagSemProc.05471.3},
  annote =	{Keywords: High performance liquid chromatography, mass spectrometry, retention time, prediction, peptide, DNA, support vector regression}
}
Document
DOI: 10.4230/DagSemProc.05471.13
OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics

Authors: Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, Eva Lange, Ole Schulz-Trieglaff, Marc Sturm, and Nico Pfeifer

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
In the talk we describe the freely available software library OpenMS which is currently under development at the Freie Universität Berlin and the Eberhardt-Karls Universität Tübingen. We give an overview of the goals and problems in differential proteomics with HPLC and then describe in detail the implemented approaches for signal processing, peak detection and data reduction currently employed in OpenMS. After this we describe methods to identify the differential expression of peptides and propose strategies to avoid MS/MS identification of peptides of interest. We give an overview of the capabilities and design principles of OpenMS and demonstrate its ease of use. Finally we describe projects in which OpenMS will be or was already deployed and thereby demonstrate its versatility.
Cite as

Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, Eva Lange, Ole Schulz-Trieglaff, Marc Sturm, and Nico Pfeifer. OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{reinert_et_al:DagSemProc.05471.13,
  author =	{Reinert, Knut and Kohlbacher, Oliver and Gr\"{o}pl, Clemens and Lange, Eva and Schulz-Trieglaff, Ole and Sturm, Marc and Pfeifer, Nico},
  title =	{{OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--7},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.13},
  URN =		{urn:nbn:de:0030-drops-5463},
  doi =		{10.4230/DagSemProc.05471.13},
  annote =	{Keywords: Proteomics, C++, Differential expression}
}
Document
DOI: 10.4230/DagSemProc.05471.1
05471 Abstract Collection – Computational Proteomics

Authors: Christian G. Huber, Oliver Kohlbacher, and Knut Reinert

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
From 20.11.05 to 25.11.05, the Dagstuhl Seminar 05471 ``Computational Proteomics'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Christian G. Huber, Oliver Kohlbacher, and Knut Reinert. 05471 Abstract Collection – Computational Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{huber_et_al:DagSemProc.05471.1,
  author =	{Huber, Christian G. and Kohlbacher, Oliver and Reinert, Knut},
  title =	{{05471 Abstract Collection – Computational Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--15},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.1},
  URN =		{urn:nbn:de:0030-drops-5569},
  doi =		{10.4230/DagSemProc.05471.1},
  annote =	{Keywords: Proteomics, mass spectrometry, MALDI, HPLC-MS, differential expression, clinical proteomics, quantitation, identification}
}
Document
DOI: 10.4230/DagSemProc.05471.2
05471 Executive Summary – Computational Proteomics

Authors: Christian G. Huber, Oliver Kohlbacher, and Knut Reinert

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
The Dagstuhl Seminar on Computational Proteomics brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface between experiment and theory. This interdisciplinary exchange covered a wide range of topics, from new experimental methods resulting in more complex data we will have to expect in the future to purely theoretical studies of what level of experimental accuracy is required in order to solve certain problems. A particular focus was also on the application side, where the participants discussed more complex experimental methodologies that are enabled by more sophisticated computational techniques. Quantitative aspects of protein expression analysis as well as posttranslational modifications in the context of disease development and diagnosis were discussed. The seminar sparked a number of new ideas and collaborations and resulted in joint grant applications and publications.
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Christian G. Huber, Oliver Kohlbacher, and Knut Reinert. 05471 Executive Summary – Computational Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{huber_et_al:DagSemProc.05471.2,
  author =	{Huber, Christian G. and Kohlbacher, Oliver and Reinert, Knut},
  title =	{{05471 Executive Summary – Computational Proteomics}},
  booktitle =	{Computational Proteomics},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.2},
  URN =		{urn:nbn:de:0030-drops-5406},
  doi =		{10.4230/DagSemProc.05471.2},
  annote =	{Keywords: Proteomics, mass spectrometry, MALDI, HPLC-MS, differential expression, clinical proteomics, quantitation, identification}
}
Document
DOI: 10.4230/DagSemProc.05471.4
An Algorithm for Feature Finding in LC/MS Raw Data

Authors: Clemens Gröpl

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
Liquid chromatography coupled with mass spectrometry is an established method in shotgun proteomics. A key step in the data processing pipeline is to transform the raw data acquired by the mass spectrometer into a list of features. In this context, a emph{feature} is defined as the two-dimensional integration with respect to retention time (RT) and mass-over-charge (m/z) of the eluting signal belonging to a single charge variant of a measurand (e.g., a peptide). Features are characterized by attributes like average mass-to-charge ratio, centroid retention time, intensity, and quality. We present a new algorithm for feature finding which has been developed as a part of a combined experimental and algorithmic approach to absolutely quantify proteins from complex samples with unprecedented precision. The method was applied to the analysis of myoglobin in human blood serum, which is an important diagnostic marker for myocardial infarction. Our approach was able to determine the absolute amount of myoglobin in a serum sample through a series of standard addition experiments with a relative error of 2.5\%. It compares favorably to a manual analysis of the same data set since we could improve the precision and conduct the whole analysis pipeline in a small fraction of the time. We anticipate that our automatic quantitation method will facilitate further absolute or relative quantitation of even more complex peptide samples. The algorithm was implemented in the publicly available software framework OpenMS (www.OpenMS.de)
Cite as

Clemens Gröpl. An Algorithm for Feature Finding in LC/MS Raw Data. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{gropl:DagSemProc.05471.4,
  author =	{Gr\"{o}pl, Clemens},
  title =	{{An Algorithm for Feature Finding in LC/MS Raw Data}},
  booktitle =	{Computational Proteomics},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.4},
  URN =		{urn:nbn:de:0030-drops-5341},
  doi =		{10.4230/DagSemProc.05471.4},
  annote =	{Keywords: Computational Proteomics, Quantitative Analysis, Liquid Chromatography, Mass Spectrometry, Algorithm, Software}
}
Document
DOI: 10.4230/DagSemProc.05471.5
Combinatorial Approaches for Mass Spectra Recalibration

Authors: Sebastian Böcker and Veli Mäkinen

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating mass spectra have to be robust with respect to wrongly assigned peaks, as well as efficient due to the amount of mass spectrometry data. The recalibration of mass spectra leads us to the problem of finding an optimal matching between mass spectra under measurement errors. We have developed two deterministic methods that allow robust computation of such a matching: The first approach uses a computational geometry interpretation of the problem, and tries to find two parallel lines with constant distance that stab a maximal number of points in the plane. The second approach is based on finding a maximal common approximate subsequence, and improves existing algorithms by one order of magnitude exploiting the sequential nature of the matching problem. We compare our results to a computational geometry algorithm using a topological line-sweep.
Cite as

Sebastian Böcker and Veli Mäkinen. Combinatorial Approaches for Mass Spectra Recalibration. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{bocker_et_al:DagSemProc.05471.5,
  author =	{B\"{o}cker, Sebastian and M\"{a}kinen, Veli},
  title =	{{Combinatorial Approaches for Mass Spectra Recalibration}},
  booktitle =	{Computational Proteomics},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.5},
  URN =		{urn:nbn:de:0030-drops-5455},
  doi =		{10.4230/DagSemProc.05471.5},
  annote =	{Keywords: Mass spectrometry recalibration computational geometry}
}
Document
DOI: 10.4230/DagSemProc.05471.6
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins

Authors: Nathanaël Delmotte, Bettina Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph Klein, and Christian G. Huber

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
The serum complexity makes the absolute quantitative analysis of medium to low-abundant proteins very challenging. Tens of thousands proteins are present in human serum and dispersed over an extremely wide dynamic range. The reliable identification and quantitation of proteins, which are potential biomarkers of disease, in serum or plasma as matrix still represents one of the most difficult analytical challenges. The difficulties arise from the presence of a few, but highly abundant proteins in serum and from the non-availability of isotope-labeled proteins, which serve to calibrate the method and to account for losses during sample preparation. For the absolute quantitation of serum proteins, we have developed an analytical scheme based on first-dimension separation of the intact proteins by anion-exchange high-performance liquid chromatography (HPLC), followed by proteolytic digestion and second-dimension separation of the tryptic peptides by reversed-phase HPLC in combination with electrospray ionization mass spectrometry (ESI-MS). The potential of mass spectrometric peptide identification in complex mixtures by means of peptide mass fingerprinting (PMF) and peptide fragment fingerprinting (PFF) was evaluated and compared utilizing synthetic mixtures of commercially available proteins and electrospray-ion trap- or electrospray time-of-flight mass spectrometers. While identification of peptides by PFF is fully supported by automated spectrum interpretation and database search routines, reliable identification by PMF still requires substantial efforts of manual calibration and careful data evaluation in order to avoid false positives. Quantitation of the identified peptides, however, is preferentially performed utilizing full-scan mass spectral data typical of PMF. Algorithmic solutions for PMF that incorporate both recalibration and automated feature finding on the basis of peak elution profiles and isotopic patterns are therefore highly desirable in order to speed up the process of data evaluation and calculation of quantitative results. Calibration for quantitative analysis of serum proteins was performed upon addition of known amounts of authentic protein to the serum sample. This was essential for the analysis of human serum samples, for which isotope-labeled protein standards are usually not available. We present the application of multidimensional HPLC-ESI-MS to the absolute quantitative analysis of myoglobin in human serum, a very sensitive biomarker for myocardial infarction. It was possible to determine myoglobin concentrations in human serum down to 100-500 ng/mL. Calibration graphs were linear over at least one order of magnitude and the relative standard deviation of the method ranged from 7-15%.
Cite as

Nathanaël Delmotte, Bettina Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph Klein, and Christian G. Huber. Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{delmotte_et_al:DagSemProc.05471.6,
  author =	{Delmotte, Nathana\"{e}l and Mayr, Bettina and Leinenbach, Andreas and Reinert, Knut and Kohlbacher, Oliver and Klein, Christoph and Huber, Christian G.},
  title =	{{Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.6},
  URN =		{urn:nbn:de:0030-drops-5397},
  doi =		{10.4230/DagSemProc.05471.6},
  annote =	{Keywords: RP-HPLC, monolith, Mascot, Myoglobin, Absolute quantitation, Serum}
}
Document
DOI: 10.4230/DagSemProc.05471.7
Future Challenges in Proteomics

Authors: Hartmut Schlüter

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
The benefits of the present proteomic approaches for the life science community are limited by 3 major problems. 1. The identification of proteins, regardless whether the peptide mass fingerprint or the shot-gun approach is used, usually is based on an incomplete set of peptides leaving large parts of the full amino acid sequence and other structural details of the original protein species in the dark; 2. Missing validation of many of the identified proteins by orthogonal biological experiments thus risking false positive results; 3. Missing standardization in nomenclature. In sum these problems may hinder progress in life science projects employing proteomic strategies and may be especially risky for system biology approaches since the ambiguities resulting from the above mentioned problems may cause wrong models. It is recommended to guide future proteome analytical investigations by a hypothesis and to focus to a smaller number of proteins which should ideally be analyzed in detail covering 100 % sequence coverage as well as all posttranslational modifications and will allow validation by additional biological experiments.
Cite as

Hartmut Schlüter. Future Challenges in Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{schluter:DagSemProc.05471.7,
  author =	{Schl\"{u}ter, Hartmut},
  title =	{{Future Challenges in Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.7},
  URN =		{urn:nbn:de:0030-drops-5449},
  doi =		{10.4230/DagSemProc.05471.7},
  annote =	{Keywords: Protein species, proteome, identification}
}
Document
DOI: 10.4230/DagSemProc.05471.8
Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools

Authors: Hansjörg Toll, Peter Berger, Andreas Hofmann, Andreas Hildebrandt, Herbert Oberacher, Hans Peter Lenhof, and Christian G. Huber

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
Due to their extensive structural heterogeneity, the elucidation of glycosylation patterns in glycoproteins such as the subunits of chorionic gonadotropin (CG), CG-alpha and CG-beta remains one of the most challenging problems in the proteomic analysis of posttranslational modifications. In consequence, glycosylation is usually studied after decomposition of the intact proteins to the proteolytic peptide level. However, by this approach all information about the combination of the different glycopeptides in the intact protein is lost. In this study we have, therefore, attempted to combine the results of glycan identification after tryptic digestion with molecular mass measurements on the intact glycoproteins. Despite the extremely high number of possible combinations of the glycans identified in the tryptic peptides by high-performance liquid chromatography-mass spectrometry (> 1000 for CG-alpha and > 10.000 for CG-beta), the mass spectra of intact CG-alpha and CG-beta revealed only a limited number of glycoforms present in CG preparations from pools of pregnancy urines. Peak annotations for CG-alpha were performed with the help of an algorithm that generates a database containing all possible modifications of the proteins (inclusive possible artificial modifications such as oxidation or truncation) and subsequent searches for combinations fitting the mass difference between the polypeptide backbone and the measured molecular masses. Fourteen different glycoforms of CG-alpha, including methionine-oxidized and N-terminally truncated forms, were readily identified. For CG-beta, however, the relatively high mass accuracy of ± 2 Da was still insufficient to unambiguously assign the possible combinations of posttranslational modifications. Finally, the mass spectrometric fingerprints of the intact molecules were shown to be very useful for the characterization of glycosylation patterns in different CG preparations.
Cite as

Hansjörg Toll, Peter Berger, Andreas Hofmann, Andreas Hildebrandt, Herbert Oberacher, Hans Peter Lenhof, and Christian G. Huber. Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{toll_et_al:DagSemProc.05471.8,
  author =	{Toll, Hansj\"{o}rg and Berger, Peter and Hofmann, Andreas and Hildebrandt, Andreas and Oberacher, Herbert and Lenhof, Hans Peter and Huber, Christian G.},
  title =	{{Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools}},
  booktitle =	{Computational Proteomics},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.8},
  URN =		{urn:nbn:de:0030-drops-5431},
  doi =		{10.4230/DagSemProc.05471.8},
  annote =	{Keywords: Liquid chromatography, mass spectrometry, glycoproteins, glycosylation, peak annotation}
}
Document
DOI: 10.4230/DagSemProc.05471.9
High-accuracy peak picking of proteomics data

Authors: Eva Lange, Clemens Gröpl, Oliver Kohlbacher, and Andreas Hildebrandt

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
A new peak picking algorithm for the analysis of mass spectrometric (MS) data is presented. It is independent of the underlying machine or ionization method, and is able to resolve highly convoluted and asymmetric signals. The method uses the multiscale nature of spectrometric data by first detecting the mass peaks in the wavelet-transformed signal before a given asymmetric peak function is fitted to the raw data. In an optional third stage, the resulting fit can be further improved using techniques from nonlinear optimization. In contrast to currently established techniques (e.g. SNAP, Apex) our algorithm is able to separate overlapping peaks of multiply charged peptides in ESI-MS data of low resolution. Its improved accuracy with respect to peak positions makes it a valuable preprocessing method for MS-based identification and quantification experiments. The method has been validated on a number of different annotated test cases, where it compares favorably in both runtime and accuracy with currently established techniques. An implementation of the algorithm is freely available in our open source framework OpenMS (www.open-ms.de).
Cite as

Eva Lange, Clemens Gröpl, Oliver Kohlbacher, and Andreas Hildebrandt. High-accuracy peak picking of proteomics data. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{lange_et_al:DagSemProc.05471.9,
  author =	{Lange, Eva and Gr\"{o}pl, Clemens and Kohlbacher, Oliver and Hildebrandt, Andreas},
  title =	{{High-accuracy peak picking of proteomics data}},
  booktitle =	{Computational Proteomics},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.9},
  URN =		{urn:nbn:de:0030-drops-5358},
  doi =		{10.4230/DagSemProc.05471.9},
  annote =	{Keywords: Mass spectrometry, peak detection, peak picking}
}
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