Popitam: Towards New Heuristic Strategies to Improve Protein Identification from Tandem Mass Spectrometry Data

Swiss Institute of Bioinformatics, Geneva, Switzerland.
PROTEOMICS (Impact Factor: 3.81). 06/2003; 3(6):870-8. DOI: 10.1002/pmic.200300402
Source: PubMed


In recent years, proteomics research has gained importance due to increasingly powerful techniques in protein purification, mass spectrometry and identification, and due to the development of extensive protein and DNA databases from various organisms. Nevertheless, current identification methods from spectrometric data have difficulties in handling modifications or mutations in the source peptide. Moreover, they have low performance when run on large databases (such as genomic databases), or with low quality data, for example due to bad calibration or low fragmentation of the source peptide. We present a new algorithm dedicated to automated protein identification from tandem mass spectrometry (MS/MS) data by searching a peptide sequence database. Our identification approach shows promising properties for solving the specific difficulties enumerated above. It consists of matching theoretical peptide sequences issued from a database with a structured representation of the source MS/MS spectrum. The representation is similar to the spectrum graphs commonly used by de novo sequencing software. The identification process involves the parsing of the graph in order to emphasize relevant sections for each theoretical sequence, and leads to a list of peptides ranked by a correlation score. The parsing of the graph, which can be a highly combinatorial task, is performed by a bio-inspired algorithm called Ant Colony Optimization algorithm.

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    • "The number of available blind database search algorithms increased substantially during the last years. Sequence-tag based methods filter the database and substitute tag mismatches by introduced modifications [52] [53] [54]. MODa goes a step further and adds spectral alignment yielding better performances and allows identifying multiple unknown PTMs on a peptide [51]. "
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    ABSTRACT: The investigation of post-translational modifications (PTMs) represents one of the main research focuses for the study of protein function and cell signaling. Mass spectrometry instrumentation with increasing sensitivity, improved protocols for PTM enrichment and recently established pipelines for high-throughput experiments allow large-scale identification and quantification of several PTM types. This review addresses the concurrently emerging challenges for the computational analysis of the resulting data and presents PTM-centered approaches for spectra identification, statistical analysis, multivariate analysis and data interpretation. We furthermore discuss the potential of future developments that will help to gain deep insight into the PTM-ome and its biological role in cells. Copyright © 2015. Published by Elsevier B.V.
    Journal of Proteomics 07/2015; 129. DOI:10.1016/j.jprot.2015.07.016 · 3.89 Impact Factor
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    • "In the present study, we have examined tyrosine nitration of mouse liver mitochondrial proteins after treatment with peroxynitrite followed by 1D and 2D SDS gel electrophoresis, Western blot analysis using an anti-nitrotyrosine antibody, and LC-MS/MS analysis of ingel tryptic digests of the nitrated protein samples. Several algorithms such as Sequest and Popitam were utilized to identify proteins and search post-translational modifications, including tyrosine nitration, based on tandem mass spectrometry data (MS/MS spectra) and peptide sequence databases [10]. On the basis of our initial findings, we focused on the tyrosine nitration of carbamoyl phosphate synthetase 1 (CPS1) in mouse mitochondria. "
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    ABSTRACT: Mitochondria are the primary locus for the generation of reactive nitrogen species including peroxynitrite and subsequent protein tyrosine nitration. Protein tyrosine nitration may have important functional and biological consequences such as alteration of enzyme catalytic activity. In the present study, mouse liver mitochondria were incubated with peroxynitrite, and the mitochondrial proteins were separated by 1D and 2D gel electrophoresis. Nitrotyrosinylated proteins were detected with an anti-nitrotyrosine antibody. One of the major proteins nitrated by peroxynitrite was carbamoyl phosphate synthetase 1 (CPS1) as identified by LC-MS protein analysis and Western blotting. The band intensity of nitration normalized to CPS1 was increased in a peroxynitrite concentration-dependent manner. In addition, CPS1 activity was decreased by treatment with peroxynitrite in a peroxynitrite concentration- and time-dependent manner. The decreased CPS1 activity was not recovered by treatment with reduced glutathione, suggesting that the decrease of the CPS1 activity is due to tyrosine nitration rather than cysteine oxidation. LC-MS analysis of in-gel digested samples, and a Popitam-based modification search located 5 out of 36 tyrosine residues in CPS1 that were nitrated. Taken together with previous findings regarding CPS1 structure and function, homology modeling of mouse CPS1 suggested that nitration at Y1450 in an α-helix of allosteric domain prevents activation of CPS1 by its activator, N-acetyl-l-glutamate. In conclusion, this study demonstrated the tyrosine nitration of CPS1 by peroxynitrite and its functional consequence. Since CPS1 is responsible for ammonia removal in the urea cycle, nitration of CPS1 with attenuated function might be involved in some diseases and drug-induced toxicities associated with mitochondrial dysfunction.
    Biochemical and Biophysical Research Communications 02/2012; 420(1):54-60. DOI:10.1016/j.bbrc.2012.02.114 · 2.30 Impact Factor
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    • "Currently, four identification software packages can be used within swissPIT: Phenyx (GeneBio SA) (Colinge 2003), Popitam (Hernandez 2003), X! Tandem (Craig 2004), and InsPecT (Tanner 2005). The choice of these first four algorithms has been motivated by a number of factors, including their popularity, their known efficiency and their implementation of various search strategies (Hernandez 2005). "
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    ABSTRACT: Proteomics is currently one of the most promising fields in bioinformatics as it provides important insights into the protein function of organisms. Mass spectrometry is one of the techniques to study the proteome, and several software tools exist for this purpose. We provide an extendable software platform called swissPIT that combines different existing tools and exploits Grid infrastructures to speed up the data analysis process for the proteomics pipeline.
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