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Zhong J, Sun Y, Xie M, Peng W, Zhang C, Wu FX, Wang J. Proteoform characterization based on top-down mass spectrometry. Brief Bioinform 2020; 22:1729-1750. [PMID: 32118252 DOI: 10.1093/bib/bbaa015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
Proteins are dominant executors of living processes. Compared to genetic variations, changes in the molecular structure and state of a protein (i.e. proteoforms) are more directly related to pathological changes in diseases. Characterizing proteoforms involves identifying and locating primary structure alterations (PSAs) in proteoforms, which is of practical importance for the advancement of the medical profession. With the development of mass spectrometry (MS) technology, the characterization of proteoforms based on top-down MS technology has become possible. This type of method is relatively new and faces many challenges. Since the proteoform identification is the most important process in characterizing proteoforms, we comprehensively review the existing proteoform identification methods in this study. Before identifying proteoforms, the spectra need to be preprocessed, and protein sequence databases can be filtered to speed up the identification. Therefore, we also summarize some popular deconvolution algorithms, various filtering algorithms for improving the proteoform identification performance and various scoring methods for localizing proteoforms. Moreover, commonly used methods were evaluated and compared in this review. We believe our review could help researchers better understand the current state of the development in this field and design new efficient algorithms for the proteoform characterization.
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Affiliation(s)
- Jiancheng Zhong
- College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China
| | - Yusui Sun
- College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China
| | - Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China
| | - Wei Peng
- Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chushu Zhang
- College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China
| | - Fang-Xiang Wu
- College of Engineering and the Department of Computer Science at University of Saskatchewan, Saskatoon, Canada
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University, Changsha, Hunan, China
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Palmblad M, Lamprecht AL, Ison J, Schwämmle V. Automated workflow composition in mass spectrometry-based proteomics. Bioinformatics 2019; 35:656-664. [PMID: 30060113 PMCID: PMC6378944 DOI: 10.1093/bioinformatics/bty646] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 11/28/2022] Open
Abstract
Motivation Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design. Results We provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools’ semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logically and semantically equivalent workflows for four use cases representing frequent tasks in MS-based proteomics. Indeed we found that the results computed by the workflows could vary considerably, emphasizing the benefits of a framework that facilitates their systematic exploration. Availability and implementation The project files and workflows are available from https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, RC Leiden, The Netherlands
| | - Anna-Lena Lamprecht
- Department of Information and Computing Sciences, Utrecht University, CC Utrecht, The Netherlands
| | - Jon Ison
- National Life Science Supercomputing Center, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
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3
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Brademan DR, Riley NM, Kwiecien NW, Coon JJ. Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications. Mol Cell Proteomics 2019; 18:S193-S201. [PMID: 31088857 PMCID: PMC6692776 DOI: 10.1074/mcp.tir118.001209] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/21/2019] [Indexed: 11/06/2022] Open
Abstract
Here we present IPSA, an innovative web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. A tool for the scientific community, IPSA can visualize peptides collected using a wide variety of experimental and instrumental configurations. Annotated spectra are customizable via a selection of interactive features and can be exported as editable scalable vector graphics to aid in the production of publication-quality figures. Single spectra can be analyzed through provided web forms, whereas data for multiple peptide spectral matches can be uploaded using the Proteomics Standards Initiative file formats mzTab, mzIdentML, and mzML. Alternatively, peptide identifications and spectral data can be provided using generic file formats. IPSA provides supports for annotating spectra collecting using negative-mode ionization and facilitates the characterization of experimental MS/MS performance through the optional export of fragment ion statistics from one to many peptide spectral matches. This resource is made freely accessible at http://interactivepeptidespectralannotator.com, whereas the source code and user guides are available at https://github.com/coongroup/IPSA for private hosting or custom implementations.
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Affiliation(s)
- Dain R Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; Genome Center of Wisconsin, Madison, WI 53706
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; Genome Center of Wisconsin, Madison, WI 53706
| | - Nicholas W Kwiecien
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; Genome Center of Wisconsin, Madison, WI 53706
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; Morgridge Institute for Research, Madison, WI 53715; Genome Center of Wisconsin, Madison, WI 53706; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706.
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4
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Perego M, Maurer M, Wang JX, Shaffer S, Müller AC, Parapatics K, Li L, Hristova D, Shin S, Keeney F, Liu S, Xu X, Raj A, Jensen JK, Bennett KL, Wagner SN, Somasundaram R, Herlyn M. A slow-cycling subpopulation of melanoma cells with highly invasive properties. Oncogene 2018; 37:302-312. [PMID: 28925403 PMCID: PMC5799768 DOI: 10.1038/onc.2017.341] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/02/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2022]
Abstract
Melanoma is a heterogeneous tumor with different subpopulations showing different proliferation rates. Slow-cycling cells were previously identified in melanoma, but not fully biologically characterized. Using the label-retention method, we identified a subpopulation of slow-cycling cells, defined as label-retaining cells (LRC), with strong invasive properties. We demonstrate through live imaging that LRC are leaving the primary tumor mass at a very early stage and disseminate to peripheral organs. Through global proteome analyses, we identified the secreted protein SerpinE2/protease nexin-1 as causative for the highly invasive potential of LRC in melanomas.
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Affiliation(s)
- M Perego
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - M Maurer
- Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - J X Wang
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - A C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - K Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L Li
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - D Hristova
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Shin
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - F Keeney
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Liu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - X Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - A Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - J K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - K L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - S N Wagner
- Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - R Somasundaram
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - M Herlyn
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
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5
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Barsnes H, Vaudel M, Martens L. JSparklines: Making tabular proteomics data come alive. Proteomics 2015; 15:1428-31. [DOI: 10.1002/pmic.201400356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/15/2014] [Accepted: 11/20/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Harald Barsnes
- Proteomics Unit, Department of Biomedicine; University of Bergen; Norway
| | - Marc Vaudel
- Proteomics Unit, Department of Biomedicine; University of Bergen; Norway
| | - Lennart Martens
- Department of Medical Protein Research; Ghent University; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
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6
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Quandt A, Espona L, Balasko A, Weisser H, Brusniak MY, Kunszt P, Aebersold R, Malmström L. Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:63-76. [PMID: 23467006 PMCID: PMC3898926 DOI: 10.1016/j.bbapap.2013.02.032] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 02/05/2013] [Accepted: 02/22/2013] [Indexed: 12/23/2022]
Abstract
Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
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Affiliation(s)
- Yasset Perez-Riverol
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba
| | - Rui Wang
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Markus Müller
- Proteome Informatics Group, Swiss Institute of Bioinformatics, CMU - 1, rue Michel Servet CH-1211 Geneva, Switzerland
| | - Vladimir Vesada
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba
| | - Juan Antonio Vizcaíno
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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8
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Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids 2013; 44:1129-37. [PMID: 23377569 DOI: 10.1007/s00726-012-1455-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 12/26/2012] [Indexed: 12/19/2022]
Abstract
With the growing interest in the field of proteomics, the amount of publicly available proteome resources has also increased dramatically. This means that there are many useful resources available for almost all aspects of a proteomics experiment. However, it remains vital to use the right resource, for the right purpose, at the right time. This review is therefore meant to aid the reader in obtaining an overview of the available resources and their application, thus providing the necessary background to choose the appropriate resources for the experiment at hand. Many of the resources are also taking advantage of so-called crowdsourcing to maximize the potential of the resource. What this means and how this can improve future experiments will also be discussed. The text roughly follows the steps involved in a proteomics experiment, starting with the planning of the experiment, via the processing of the data and the analysis of the results, to the community-wide sharing of the produced data.
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Niedermeyer THJ, Strohalm M. mMass as a software tool for the annotation of cyclic peptide tandem mass spectra. PLoS One 2012; 7:e44913. [PMID: 23028676 PMCID: PMC3441486 DOI: 10.1371/journal.pone.0044913] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/09/2012] [Indexed: 11/19/2022] Open
Abstract
Natural or synthetic cyclic peptides often possess pronounced bioactivity. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and the complex fragmentation patterns observed. Even though several software tools for cyclic peptide tandem mass spectra annotation have been published, these tools are still unable to annotate a majority of the signals observed in experimentally obtained mass spectra. They are thus not suitable for extensive mass spectrometric characterization of these compounds. This lack of advanced and user-friendly software tools has motivated us to extend the fragmentation module of a freely available open-source software, mMass (http://www.mmass.org), to allow for cyclic peptide tandem mass spectra annotation and interpretation. The resulting software has been tested on several cyanobacterial and other naturally occurring peptides. It has been found to be superior to other currently available tools concerning both usability and annotation extensiveness. Thus it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides.
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10
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Perez-Riverol Y, Sánchez A, Ramos Y, Schmidt A, Müller M, Betancourt L, González LJ, Vera R, Padron G, Besada V. In silico analysis of accurate proteomics, complemented by selective isolation of peptides. J Proteomics 2011; 74:2071-82. [PMID: 21658481 DOI: 10.1016/j.jprot.2011.05.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/06/2011] [Accepted: 05/22/2011] [Indexed: 01/28/2023]
Abstract
Protein identification by mass spectrometry is mainly based on MS/MS spectra and the accuracy of molecular mass determination. However, the high complexity and dynamic ranges for any species of proteomic samples, surpass the separation capacity and detection power of the most advanced multidimensional liquid chromatographs and mass spectrometers. Only a tiny portion of signals is selected for MS/MS experiments and a still considerable number of them do not provide reliable peptide identification. In this article, an in silico analysis for a novel methodology of peptides and proteins identification is described. The approach is based on mass accuracy, isoelectric point (pI), retention time (t(R)) and N-terminal amino acid determination as protein identification criteria regardless of high quality MS/MS spectra. When the methodology was combined with the selective isolation methods, the number of unique peptides and identified proteins increases. Finally, to demonstrate the feasibility of the methodology, an OFFGEL-LC-MS/MS experiment was also implemented. We compared the more reliable peptide identified with MS/MS information, and peptide identified with three experimental features (pI, t(R), molecular mass). Also, two theoretical assumptions from MS/MS identification (selective isolation of peptides and N-terminal amino acid) were analyzed. Our results show that using the information provided by these features and selective isolation methods we could found the 93% of the high confidence protein identified by MS/MS with false-positive rate lower than 5%.
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Affiliation(s)
- Yasset Perez-Riverol
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cubanacán, Playa, Ciudad de la Habana, Cuba.
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11
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Ramos Y, Garcia Y, Pérez-Riverol Y, Leyva A, Padrón G, Sánchez A, Castellanos-Serra L, González LJ, Besada V. Peptide fractionation by acid pH SDS-free electrophoresis. Electrophoresis 2011; 32:1323-6. [DOI: 10.1002/elps.201000677] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 11/11/2022]
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12
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Yadav AK, Kumar D, Dash D. MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry. J Proteome Res 2011; 10:2154-60. [DOI: 10.1021/pr200031z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Amit Kumar Yadav
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi, India
| | - Dhirendra Kumar
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi, India
| | - Debasis Dash
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi, India
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Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L. compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics 2011; 12:70. [PMID: 21385435 PMCID: PMC3060842 DOI: 10.1186/1471-2105-12-70] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 03/08/2011] [Indexed: 01/10/2023] Open
Abstract
Background The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. Results In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. Conclusions As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.
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Affiliation(s)
- Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
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Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2010; 9:5112-9. [PMID: 19834897 DOI: 10.1002/pmic.200900189] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.
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Affiliation(s)
- Luisa Montecchi-Palazzi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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15
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Tsai YS, Scherl A, Shaw JL, MacKay CL, Shaffer SA, Langridge-Smith PRR, Goodlett DR. Precursor ion independent algorithm for top-down shotgun proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2154-2166. [PMID: 19773183 DOI: 10.1016/j.jasms.2009.07.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 07/29/2009] [Accepted: 07/29/2009] [Indexed: 05/28/2023]
Abstract
We present a precursor ion independent top-down algorithm (PIITA) for use in automated assignment of protein identifications from tandem mass spectra of whole proteins. To acquire the data, we utilize data-dependent acquisition to select protein precursor ions eluting from a C4-based HPLC column for collision induced dissociation in the linear ion trap of an LTQ-Orbitrap mass spectrometer. Gas-phase fractionation is used to increase the number of acquired tandem mass spectra, all of which are recorded in the Orbitrap mass analyzer. To identify proteins, the PIITA algorithm compares deconvoluted, deisotoped, observed tandem mass spectra to all possible theoretical tandem mass spectra for each protein in a genomic sequence database without regard for measured parent ion mass. Only after a protein is identified, is any difference in measured and theoretical precursor mass used to identify and locate post-translation modifications. We demonstrate the application of PIITA to data generated via our wet-lab approach on a Salmonella typhimurium outer membrane extract and compare these results to bottom-up analysis. From these data, we identify 154 proteins by top-down analysis, 73 of which were not identified in a parallel bottom-up analysis. We also identify 201 unique isoforms of these 154 proteins at a false discovery rate (FDR) of <1%.
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Affiliation(s)
- Yihsuan S Tsai
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, USA
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16
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Parikh JR, Askenazi M, Ficarro SB, Cashorali T, Webber JT, Blank NC, Zhang Y, Marto JA. multiplierz: an extensible API based desktop environment for proteomics data analysis. BMC Bioinformatics 2009; 10:364. [PMID: 19874609 PMCID: PMC2774704 DOI: 10.1186/1471-2105-10-364] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 10/29/2009] [Indexed: 11/25/2022] Open
Abstract
Background Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. Results We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. Conclusion Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.
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Affiliation(s)
- Jignesh R Parikh
- Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA, 02115, USA.
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Abstract
UNLABELLED Mass spectrometry-based proteomics stands to gain from additional analysis of its data, but its large, complex datasets make demands on speed and memory usage requiring special consideration from scripting languages. The software library 'mspire'-developed in the Ruby programming language-offers quick and memory-efficient readers for standard xml proteomics formats, converters for intermediate file types in typical proteomics spectral-identification work flows (including the Bioworks .srf format), and modules for the calculation of peptide false identification rates. AVAILABILITY Freely available at http://mspire.rubyforge.org. Additional data models, usage information, and methods available at http://bioinformatics.icmb.utexas.edu/mspire
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Affiliation(s)
- John T Prince
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
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18
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Hewel JA, Emili A. High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates. Proteomics Clin Appl 2008; 2:1422-34. [DOI: 10.1002/prca.200800030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Indexed: 12/18/2022]
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Ramos Y, Gutierrez E, Machado Y, Sánchez A, Castellanos-Serra L, González LJ, Fernández-de-Cossio J, Pérez-Riverol Y, Betancourt L, Gil J, Padrón G, Besada V. Proteomics based on peptide fractionation by SDS-free PAGE. J Proteome Res 2008; 7:2427-34. [PMID: 18422305 DOI: 10.1021/pr700840y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we demonstrate the usefulness of peptide fractionation by SDS-free polyacrylamide gel electrophoresis and its applicability to proteomics studies. In the absence of SDS, the driving force for the electrophoretic migration toward the anode is supplied by negatively charged acidic amino acid residues and other residues as phosphate, sulfate and sialic acid, while the resulting mobility depends on both the charge and the molecular mass of the peptides. A straightforward method was achieved for SDS-PAGE of proteins, enzyme digestion, peptide transfer and fractionation by SDS-free PAGE, which was named dual-fractionation polyacrylamide gel electrophoresis (DF-PAGE). This method increases the number of identified proteins 2.5-fold with respect to the proteins identified after direct analysis, and more than 80% of assigned peptides were found in unique SDS-free gel slices. A vast majority of identified peptides (93%) have p I values below 7.0, and 7% have p I values between 7.0 and 7.35. Peptide digests that were derived from complex protein mixtures were in consequence simplified as peptides that are positively charged are not recovered in the present conditions. The analysis of a membrane protein extract from Neisseria meningitidis by this approach allowed the identification of 97 proteins, including low-abundance components.
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Affiliation(s)
- Yassel Ramos
- Center for Genetic Engineering and Biotechnology, La Habana, Cuba
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20
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Affiliation(s)
- Jacques Colinge
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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21
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Pitzer E, Masselot A, Colinge J. Assessing peptidede novo sequencing algorithms performance on large and diverse data sets. Proteomics 2007; 7:3051-4. [PMID: 17683051 DOI: 10.1002/pmic.200700224] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
De novo peptide sequencing algorithms are often tested on relatively small data sets made of excellent spectra. Since there are always more and more tandem mass spectra available, we have assembled six large, reliable, and diverse (three mass spectrometer types) data sets intended for such tests and we make them accessible via a web server. To exemplify their use we investigate the performance of Lutefisk, PepNovo, and PepNovoTag, three well-established peptide de novo sequencing programs.
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Affiliation(s)
- Erik Pitzer
- Bioinformatics Department, Upper Austria University of Applied Sciences at Hagenberg, Hagenberg, Austria
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22
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Abstract
We present new statistical models of peptide fragment peak intensities that achieve unprecedented accuracy, and we discuss their application to the problem of scoring in database searching or peptide de novo sequencing. The models, made available via open-source computer programs, are very general and can potentially improve any intensity-based scoring.
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Affiliation(s)
- Jacques Colinge
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 19/3, A-1090 Vienna, Austria.
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23
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Rinner O, Mueller LN, Hubálek M, Müller M, Gstaiger M, Aebersold R. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol 2007; 25:345-52. [PMID: 17322870 DOI: 10.1038/nbt1289] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 01/18/2007] [Indexed: 11/08/2022]
Abstract
Biological systems are controlled by protein complexes that associate into dynamic protein interaction networks. We describe a strategy that analyzes protein complexes through the integration of label-free, quantitative mass spectrometry and computational analysis. By evaluating peptide intensity profiles throughout the sequential dilution of samples, the MasterMap system identifies specific interaction partners, detects changes in the composition of protein complexes and reveals variations in the phosphorylation states of components of protein complexes. We use the complexes containing the human forkhead transcription factor FoxO3A to demonstrate the validity and performance of this technology. Our analysis identifies previously known and unknown interactions of FoxO3A with 14-3-3 proteins, in addition to identifying FoxO3A phosphorylation sites and detecting reduced 14-3-3 binding following inhibition of phosphoinositide-3 kinase. By improving specificity and sensitivity of interaction networks, assessing post-translational modifications and providing dynamic interaction profiles, the MasterMap system addresses several limitations of current approaches for protein complexes.
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Affiliation(s)
- Oliver Rinner
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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