Ursgal - Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis

Please note that, due to significant reorganization of UController functions as well as some uparams, compatibility of v0.6.0 with previous versions is not given in all cases. Most likely, your previous results will not be recognized, i.e. previously executed runs will be executed again. Please consider this before updating to v0.6.0, check the Changelog or ask us if you have any doubts. We are sorry for the inconvenience but changes were necessary for further development. If you want to continue using (and modifying) v0.5.0 you can use the branch v0.5.0.

Ursgal is a Python module that offers a generalized interface to common bottom-up proteomics tools, e.g.

1. Peptide spectrum matching with up to eight different search engines (some available in multiple versions), including three open modification search engines
2. Evaluation and post processing of search results with up to two different engines
3. Integration of search results from different search engines
4. De novo sequencing with up to two different search engines
5. Miscellaneous tools including the creation of a target decoy database as well as filtering, sanitizing and visualizing of results

Proteomics data integration has become a broad field with a variety of programs offering innovative algorithms to analyze increasing amounts of data. Unfortunately, this software diversity leads to many problems as soon as the data is analyzed using more than one algorithm for the same task. Although it was shown that the combination of multiple peptide identification algorithms yields more robust results (Nahnsen et al. 2011, Vaudel et al. 2015, Kwon et al. 2011), it is only recently that unified approaches are emerging (Vaudel et al. 2011, Wen et al. 2015); however, workflows that, for example, aim to optimize search parameters or that employ cascaded style searches (Kertesz-Farkas et al. 2015) can only be made accessible if data analysis becomes not only unified but also and most importantly scriptable. Here we introduce Ursgal, a Python interface to many commonly used bottom-up proteomics tools and to additional auxiliary programs. Complex workflows can thus be composed using the Python scripting language using a few lines of code. Ursgal is easily extensible, and we have made several database search engines (X!Tandem (Craig and Beavis 2004), OMSSA (Geer et al. 2004), MS-GF+ (Kim et al. 2010), Myrimatch (Tabb et al. 2008), MS Amanda (Dorfer et al. 2014)), statistical postprocessing algorithms (qvality (Käll et al. 2009), Percolator (Käll et al. 2008)), and one algorithm that combines statistically postprocessed outputs from multiple search engines (“combined FDR” (Jones et al. 2009)) accessible as an interface in Python. Furthermore, we have implemented a new algorithm (“combined PEP”) that combines multiple search engines employing elements of “combined FDR” (Jones et al. 2009), PeptideShaker (Vaudel et al. 2015), and Bayes’ theorem.

Kremer, L. P. M., Leufken, J., Oyunchimeg, P., Schulze, S. and Fufezan, C. (2015): Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis , Journal of Proteome research, 15, 788-. DOI:10.1021/acs.jproteome.5b00860

Get the latest version via GitHub:

https://github.com/ursgal/ursgal

as .zip package:

https://github.com/ursgal/ursgal/archive/master.zip

or via git clone URL:

https://github.com/ursgal/ursgal.git

The complete Documentation can be found at

http://ursgal.readthedocs.org/

Ursgal requires Python 3.4 or higher.

If you want to run Ursgal on a Windows system, Python 3.6 or higher is recommended.

Download Ursgal using GitHub or the zip file:

• GitHub version: Starting with this the easiest way is to clone the GitHub repo.:

  user@localhost:~$ git clone https://github.com/ursgal/ursgal.git
  

• ZIP version: Alternatively, download and extract the ursgal zip file

Install requirements:

user@localhost:~$ cd ursgal
user@localhost:~/ursgal$ pip3.4 install -r requirements.txt

Install third party engines:

user@localhost:~/ursgal$ python3.4 install_resources.py

Install Ursgal:

user@localhost:~/ursgal$ python3.4 setup.py install

(You might need administrator privileges to write in the Python site-package folder. On Linux or OS X, use `sudo python setup.py install` or write into a user folder by using this command `python setup.py install --user`. On Windows, you have to start the command line with administrator privileges.)

Run nosetests in root folder. You might need to install nose for Python3 first although it is in the requirements.txt (above) thus pip3.4 install -r requirements should have installed it already. Then just execute:

user@localhost:~/ursgal$ nosetests3

to test the package.

If you encounter any problems you can open up issues at GitHub, join the conversation at Gitter, or write an email to [email protected]. Please also check the :ref:`faq`.

For any contributions, fork us at https://github.com/ursgal/ursgal and open up pull requests! Please also check the :ref:`contribute`. Thanks!

For more detailed documentation of the modules and examples, please refer to the documentation folder or http://ursgal.readthedocs.org

Ursgal is beta and thus still contains bugs. Verify your results manually and as common practice in science, never trust a blackbox :)

Copyright 2014-2018 by authors and contributors in alphabetical order

• Christian Fufezan
• Aime B. Igiraneza
• Manuel Koesters
• Lukas P. M. Kremer
• Johannes Leufken
• Purevdulam Oyunchimeg
• Stefan Schulze
• Fengchao Yu
• Lukas Vaut

Dr. Christian Fufezan

Institute of Plant Biology and Biotechnology

Schlossplatz 8 , R 105

University of Muenster

Germany

eMail: [email protected]

Tel: +049 251 83 24861

http://www.uni-muenster.de/Biologie.IBBP.AGFufezan

Ursgal citation

Kremer, L. P. M., Leufken, J., Oyunchimeg, P., Schulze, S., and Fufezan, C. (2016) Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis Journal of Proteome research 15, 788–794, DOI:10.1021/acs.jproteome.5b00860

Full list of tools with proper citations that are integrated into Ursgal are:

• Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20 (9), 1466–1467.
• Dorfer, V.; Pichler, P.; Stranzl, T.; Stadlmann, J.; Taus, T.; Winkler, S.; Mechtler, K. MS Amanda, a Universal Identification Algorithm Optimised for High Accuracy Tandem Mass Spectra. J. Proteome Res. 2014.
• Frank, A. M.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. and Pevzner, P. A. De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry. J. Proteome Res. 2007 6:114-123.',
• Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. Open Mass Spectrometry Search Algorithm. J. Proteome res. 2004, 3 (5), 958–964.
• Hoopmann, M. R.; Zelter, A.; Johnson, R. S.; Riffle, M.; Maccoss, M. J.; Davis, T. N.; Moritz, R. L. Kojak: Efficient analysis of chemically cross-linked protein complexes. J Proteome Res 2015, 14, 2190-198
• Jones, A. R.; Siepen, J. a.; Hubbard, S. J.; Paton, N. W. Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 2009, 9 (5), 1220–1229.
• Kim, S.; Mischerikow, N.; Bandeira, N.; Navarro, J. D.; Wich, L.; Mohammed, S.; Heck, A. J. R.; Pevzner, P. A. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. MCP 2010, 2840–2852.
• Käll, L.; Canterbury, J. D.; Weston, J.; Noble, W. S.; MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nature methods 2007, 4 (11), 923–925.
• Käll, L.; Storey, J. D.; Noble, W. S. Qvality: Non-parametric estimation of q-values and posterior error probabilities. Bioinformatics 2009, 25 (7), 964–966.
• Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature methods 2017, 14, 513–520
• Leufken J, Niehues A, Sarin LP, Wessel F, Hippler M, Leidel SA, Fufezan C. pyQms enables universal and accurate quantification of mass spectrometry data. Mol Cell Proteomics 2017, 16, 1736-1745
• Ma, B. Novor: real-time peptide de novo sequencing software. J Am Soc Mass Spectrom. 2015 Nov;26(11):1885-94
• Na S, Bandeira N, Paek E. Fast multi-blind modification search through tandem mass spectrometry. Mol Cell Proteomics 2012, 11
• Reisinger, F.; Krishna, R.; Ghali, F.; Ríos, D.; Hermjakob, H.; Antonio Vizcaíno, J.; Jones, A. R. JmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics 2012, 12 (6), 790–794.
• Tabb, D. L.; Fernando, C. G.; Chambers, M. C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res. 2008, 6 (2), 654–661.
• Yu, F., Li, N., Yu, W. PIPI: PTM-Invariant Peptide Identification Using Coding Method. J Prot Res 2016, 15
• Barsnes, H., Vaudel, M., Colaert, N., Helsens, K., Sickmann, A., Berven, F. S., and Martens, L. (2011) compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics 12, 70
• Leufken, J., Niehues, A., Sarin, L. P., Wessel, F., Hippler, M., Leidel, S. A., and Fufezan, C. (2017) pyQms enables universal and accurate quantification of mass spectrometry data. Mol. Cell. Proteomics 16, 1736–1745
• Jaeger, D., Barth, J., Niehues, A., and Fufezan, C. (2014) pyGCluster, a novel hierarchical clustering approach. Bioinformatics 30, 896–898
• Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012) pymzML--Python module for high-throughput bioinformatics on mass spectrometry data. Bioinformatics 28, 1052–1053
• Kösters, M., Leufken, J., Schulze, S., Sugimoto, K., Klein, J., Zahedi, R. P., Hippler, M., Leidel, S. A., and Fufezan, C. (2018) pymzML v2.0: introducing a highly compressed and seekable gzip format. Bioinformatics,