MzJava: An open source library for mass spectrometry data processing

Horlacher, Oliver; Nikitin, Frédéric; Alocci, Davide; Mariethoz, Julien; Müller, Markus; Lisacek, Frédérique

doi:10.1016/j.jprot.2015.06.013

Cited by 26 publications

(27 citation statements)

References 37 publications

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“…It is based on a well‐defined acquisition protocol where MS/MS spectra are recorded stepwise over a large CE range. It was implemented using the MzJava class library developed and maintained by the Proteome Informatics Group . The tool manages data import and result export in several formats.…”

Section: Methodsmentioning

confidence: 99%

Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry

Alghanem

Nikitin

Stricker

et al. 2017

Rapid Comm Mass Spectrometry

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Isotopically labelled peptides can be used to optimize MRM transitions more efficiently in FIA than by searching databases. The MRMOptimizer software is MS independent and enables the post-acquisition selection of MRM parameters. Coefficients of variation for optimal CE values are lower than those obtained with the SRMAtlas approach (B2) and one additional peptide was detected. Copyright © 2017 John Wiley & Sons, Ltd.

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Section: Methodsmentioning

confidence: 99%

Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry

Alghanem

Nikitin

Stricker

et al. 2017

Rapid Comm Mass Spectrometry

View full text Add to dashboard Cite

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“…The open-source Java library mzJava from ExPASy (http://mzjava.expasy.org) supported protein digestion [18]. For the purposes of the present analysis, three proteases representing the major intestinal endoproteases were used: trypsin, chymotrypsin and pepsin (low specificity model, pH>2).…”

Section: Methodsmentioning

confidence: 99%

“…SPECLUST, a public web-based tool, was used to identify representative and reproducible peak masses that are present in a collection of spectral profiles [18]. This tool calculates the mass difference between two peaks taken from different peak lists and determines whether or not the two peaks are identical, taking into account some measurement uncertainty (σ).…”

Section: Methodsmentioning

confidence: 99%

“…This methodology follows the same general principle of existing mass spectrometry approaches but it uses whole genome data and in silico protein digestion, i.e., it does not involve any conventional experimentation. Furthermore, the analysis stands on the shoulders of well-established software tools, namely PSortB [17], mzJava [18], SPECLUST [19] and MrBayes [20]. The aim is to be able to generate a valid and manageable list of peptides that are potentially specific to each strain.…”

Section: Introductionmentioning

confidence: 99%

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Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

et al. 2016

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Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.

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“…In silico digestion is performed using the ExPASy mzJava (http://mzjava.expasy.org) library (29) and considering the major human intestinal endoproteases, i.e. trypsin, chemotrypsin and pepsin (pH < 2).…”

Section: Database Construction and Updatementioning

confidence: 99%

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

et al. 2017

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The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome. Bioactivity prediction is based on the global alignment of the automatically processed peptides with experimentally validated immunomodulatory and antiproliferative peptides, in the reference section. MAHMI provides researchers with a comparative tool for inspecting the potential immunomodulatory or antiproliferative bioactivity of new amino acidic sequences and identifying promising peptides to be further investigated. Moreover, researchers are welcome to submit new experimental evidence on peptide bioactivity, namely, empiric and structural data, as a proactive, expert means to keep the database updated and improve the implemented bioactivity prediction method. Bioactive peptides identified by MAHMI have a huge biotechnological potential, including the manipulation of aberrant immune responses and the design of new functional ingredients/foods based on the genetic sequences of the human microbiome. Hopefully, the resources provided by MAHMI will be useful to those researching gastrointestinal disorders of autoimmune and inflammatory nature, such as Inflammatory Bowel Diseases. MAHMI database is routinely updated and is available free of charge.Database URL: http://mahmi.org/

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MzJava: An open source library for mass spectrometry data processing

Cited by 26 publications

References 37 publications

Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry

Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

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