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CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies

bioinformatics 2016年第3期32卷 469-471页

作者： Chen, Jun Just, Allan C. Schwartz, Joel Hou, Lifang Jafari, Nadereh Sun, Zhifu Kocher, Jean-Pierre A. Baccarelli, Andrea Lin, Xihong Mayo Clin Div Biomed Stat & Informat Rochester MN 55905 USA Mayo Clin Ctr Individualized Med Rochester MN 55905 USA Harvard Univ Sch Publ Hlth Dept Biostat Boston MA 02115 USA Harvard Univ Sch Publ Hlth Dept Environm Hlth Boston MA 02115 USA Northwestern Univ Dept Prevent Med Evanston IL 60208 USA Northwestern Univ Robert H Lurie Comprehens Canc Ctr Feinberg Sch Med Evanston IL 60208 USA Northwestern Univ Ctr Genet Med Feinberg Sch Med Evanston IL 60208 USA

The development of the Infinium HumanMethylation450 BeadChip enables epigenome-wide association studies at a reduced cost. One observation of the 450K data is that many CpG sites the beadchip interrogates have very large measurement errors. Including these noisy CpGs will decrease the statistical power of detecting relevant associations due to multiple testing correction. We propose to use intra-class correlation coefficient (ICC), which characterizes the relative contribution of the biological variability to the total variability, to filter CpGs when technical replicates are available. We estimate the ICC based on a linear mixed effects model by pooling all the samples instead of using the technical replicates only. An ultra-fast algorithm has been developed to address the computational complexity and CpG filtering can be completed in minutes on a desktop computer for a 450K data set of over 1000 samples. Our method is very flexible and can accommodate any replicate design. Simulations and a real data application demonstrate that our whole-sample ICC method performs better than replicate-sample ICC or variance-based method.

关键词： bioinformatics software EVALUATION CPG nucleotides EPIGENETICS

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Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated Peptides

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MOLECULAR & CELLULAR PROTEOMICS 2020年第1期19卷 167-180页

作者： Larsen, Daniel Nyberg Mikkelsen, Christian Engelbrecht Kierkegaard, Mads Bereta, Grzegorz P. Nowakowska, Zuzanna Kaczmarek, Jakub Z. Potempa, Jan Hojrup, Peter Univ Southern Denmark Campusvej 55 Odense M Denmark Jagiellonian Univ Dept Microbiol Fac Biochem Biophys & Biotechnol Krakow Poland Jagiellonian Univ Malopolska Ctr Biotechnol Krakow Poland Ovodan Biotech AS Dept Res & Dev DK-5000 Odense Denmark Univ Louisville Sch Dent Dept Oral Immunol & Infect Dis 501 S Preston St Louisville KY 40292 USA

The citrullinome of P. gingivalis outer membrane vesicles (OMV) has been explored by a novel two-dimensional separation system combined with high resolution mass spectrometry and in-house build software. Analysis of OMVs from wild-type and two PPAD mutants resulted in confident discrimination based on citrullinated peptides. In the wild-type citrullinome 78 proteins were identified having a total of 161 validated citrullination sites. A single citrullination was identified in the C351A mutant and none in the ?PPAD mutant. Porphyromonas gingivalis is a key pathogen in chronic periodontitis and has recently been mechanistically linked to the development of rheumatoid arthritis via the activity of peptidyl arginine deiminase generating citrullinated epitopes in the periodontium. In this project the outer membrane vesicles (OMV) from P. gingivalis W83 wild-type (WT), a W83 knock-out mutant of peptidyl arginine deiminase (?PPAD), and a mutant strain expressing PPAD with the active site cysteine mutated to alanine (C351A), have been analyzed using a two-dimensional HFBA-based separation system combined with LC-MS. For optimal and positive identification and validation of citrullinated peptides and proteins, high resolution mass spectrometers and strict MS search criteria were utilized. This may have compromised the total number of identified citrullinations but increased the confidence of the validation. A new two-dimensional separation system proved to increase the strength of validation, and along with the use of an in-house build program, Citrullia, we establish a fast and easy semi-automatic (manual) validation of citrullinated peptides. For the WT OMV we identified 78 citrullinated proteins having a total of 161 citrullination sites. Notably, in keeping with the mechanism of OMV formation, the majority (51 out of 78) of citrullinated proteins were predicted to be exported via the inner membrane and to reside in the periplasm or being translocated to the bacterial sur

关键词： Chromatography protein identification protein modification post-translational modifications omics bacteria bioinformatics software HPLC HFBA orthogonal two-dimensional

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Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning

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MOLECULAR & CELLULAR PROTEOMICS 2019年第10期18卷 2099-2107页

作者： Guan, Shenheng Moran, Michael F. Ma, Bin Univ Waterloo David R Cheriton Sch Comp Sci Waterloo ON N2L 3G1 Canada Hosp Sick Children Program Cell Biol 686 Bay St Toronto ON M5G 0A4 Canada Hosp Sick Children SPARC BioCtr 686 Bay St Toronto ON M5G 0A4 Canada Univ Toronto Dept Mol Genet 686 Bay St Toronto ON M5G 0A4 Canada

Deep learning models for prediction of three key LC-MS/MS properties from peptide sequences were developed. The LC-MS/MS properties or behaviors are indexed retention times (iRT), MS1 or survey scan charge state distributions, and sequence ion intensities of HCD spectra. A common core deep supervised learning architecture, bidirectional long-short term memory (LSTM) recurrent neural networks was used to construct the three prediction models. Two featurization schemes were proposed and demonstrated to allow for efficient encoding of modifications. The iRT and charge state distribution models were trained with on order of 105 data points each. An HCD sequence ion prediction model was trained with 2 x 106 experimental spectra. The iRT prediction model and HCD sequence ion prediction model provide improved accuracies over the start-of-the-art models available in literature. The MS1 charge state distribution prediction model offers excellent performance. The prediction models can be used to enhance peptide identification and quantification in data-dependent acquisition and data-independent acquisition (DIA) experiments as well as to assist MRM (multiple reaction monitoring) and PRM (parallel reaction monitoring) experiment design.

关键词： Algorithms Peptides Statistics bioinformatics software bioinformatics Charge State Distribution Deep Learning Indexed Retention Time Prediction

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Sequanix: a dynamic graphical interface for Snakemake workflows

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bioinformatics 2018年第11期34卷 1934-1936页

作者： Desvillechabrol, Dimitri Legendre, Rachel Rioualen, Claire Bouchier, Christiane van Helden, Jacques Kennedy, Sean Cokelaer, Thomas Inst Pasteur Biom Pole CITECH F-75015 Paris France Inst Pasteur Bioinformat & Biostat Hub C3BI USR IP CNRS 3756 F-75015 Paris France Aix Marseille Univ INSERM TAGC UMR S 1090 F-13288 Marseille France

The Summary: We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://***), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users.

关键词： GRAPHICAL user interfaces bioinformatics software WORKFLOW software SCRIPTING languages (Computer science) DATA structures (Computer science)

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Irys Extract

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bioinformatics 2018年第1期34卷 134-136页

作者： Arielly, Rani Ebenstein, Yuval Tel Aviv Univ Sch Chem Raymond & Beverly Sackler Fac Exact Sci Ctr Nanosci & Nanotechnol IL-69978 Tel Aviv Israel

Irys Extract is a software tool for generating genomic information from data collected by the BioNano Genomics Irys platform. The tool allows the user easy access to the raw data in the form of cropped images and genetically aligned intensity profiles. The latter are also made compatible with the BED format for using with popular genomic browsers such as the UCSC Genome Browser. Availability and implementation: Irys Extract has been developed in Matlab R2015a, it was tested to work with IrysView 2.4.0.15879 and AutoDetect 2.1.4.9159, and it currently runs under Microsoft Windows operating systems (7-10). Irys Extract can be downloaded alongside its manual and a demo dataset at http://*** and https://***/site/raniarielly/. Contact: uv@*** Supplementary information: Supplementary data are available at bioinformatics online.

关键词： GENOMIC information retrieval bioinformatics software COMPUTATIONAL biology bioinformatics GENOMES

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bioinformatics - from genes to pathways

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NATURE METHODS 2004年第2期1卷 169-175页

作者： Bonetta, L Laura Bonetta is a freelance writer based in the Washington DC area lbonetta@***

Combined with the right computational tools, genomic data can uncover unknown pathways to cellular processes. Because few researchers have the resources to develop their own bioinformatics software, companies have ste... 详细信息

关键词： Genes Companies Cellular processes Pathway bioinformatics software bioinformatics

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Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition

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MOLECULAR & CELLULAR PROTEOMICS 2020年第1期19卷 181-197页

作者： Barkovits, Katalin Pacharra, Sandra Pfeiffer, Kathy Steinbach, Simone Eisenacher, Martin Marcus, Katrin Uszkoreit, Julian Ruhr Univ Bochum Fac Med Med Proteom Ctr Bochum Germany

The impact of different approaches for spectral library generation used by DIA was analyzed on identification and quantification level using a gold standard spike-in data set. We included approaches using repetitive measurements of the original samples as well as methods applying peptide and protein pre-fractionation before library generation. The comparisons show, that prefractionation generally increases the number of identified peptides and protein groups, whereas the ground truth quantification ratios could be well approximated using libraries generated by repetitive measurements. Currently data-dependent acquisition (DDA) is the method of choice for mass spectrometry-based proteomics discovery experiments, but data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirements to perform a DIA analysis is the availability of suitable spectral libraries for peptide identification and quantification. Several studies were performed addressing the evaluation of spectral library performance for protein identification in DIA measurements. But so far only few experiments estimate the effect of these libraries on the quantitative level. In this work we created a gold standard spike-in sample set with known contents and ratios of proteins in a complex protein matrix that allowed a detailed comparison of DIA quantification data obtained with different spectral library approaches. We used in-house generated sample-specific spectral libraries created using varying sample preparation approaches and repeated DDA measurement. In addition, two different search engines were tested for protein identification from DDA data and subsequent library generation. In total, eight different spectral libraries were generated, and the quantification results compared with a library free method, as well as a default DDA analysis. Not only the number of identifications on peptide and protein level in the spectral libraries and the corresponding DIA a

关键词： Mass Spectrometry Quantification Label-free quantification bioinformatics software Target identification data-independent acquisition (DIA) peptide identification proteomics spectral library

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Rust-Bio: a fast and safe bioinformatics library

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bioinformatics 2016年第3期32卷 444-446页

作者： Koester, Johannes Harvard Univ Sch Publ Hlth Dana Farber Canc Inst Ctr Funct Canc EpigenetDept Biostat & Computat B Boston MA 02215 USA Harvard Univ Sch Med Dana Farber Canc Inst Dept Med Oncol Boston MA 02215 USA

We present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of bioinformatics algorithms and data structures with a focus on sequence analysis.

关键词： bioinformatics software EVALUATION PROGRAMMING languages (Electronic computers)

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I-PV: a CIRCOS module for interactive protein sequence visualization

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bioinformatics 2016年第3期32卷 447-449页

作者： Tanyalcin, Ibrahim Al Assaf, Carla Gheldof, Alexander Stouffs, Katrien Lissens, Willy Jansen, Anna C. UZ Brussel Ctr Med Genet Brussels Belgium Vrije Univ Brussel Neurogenet Res Grp Brussels Belgium Katholieke Univ Leuven Ctr Human Genet B-3000 Leuven Belgium Univ Hosp Leuven B-3000 Leuven Belgium Vrije Univ Brussel Reprod Genet & Regenerat Med Brussels Belgium UZ Brussel Dept Pediat Pediat Neurol Unit Brussels Belgium

Today's genome browsers and protein databanks supply vast amounts of information about proteins. The challenge is to concisely bring together this information in an interactive and easy to generate format.

关键词： bioinformatics software EVALUATION AMINO acid sequence

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Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

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MOLECULAR & CELLULAR PROTEOMICS 2019年第4期18卷 786-795页

作者： Mueller, Franze Kolbowski, Lars Bernhardt, Oliver M. Reiter, Lukas Rappsilber, Juri Tech Univ Berlin Inst Biotechnol Bioanalyt D-13355 Berlin Germany Univ Edinburgh Wellcome Ctr Cell Biol Sch Biol Sci Edinburgh EH9 3BF Midlothian Scotland Biognosys CH-8952 Zurich Switzerland

Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of E. coil cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.

关键词： Protein Cross-linking* Label-free quantification Mass Spectrometry Quantification bioinformatics software Data independent acquisition Reproducibility Spectronaut Xi

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