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Lange S, Rosenkrands I, Stein R, Andersen P, Kaufmann SHE, Jungblut PR. Analysis of protein species differentiation among mycobacterial low-Mr-secreted proteins by narrow pH range Immobiline gel 2-DE-MALDI-MS. J Proteomics 2013; 97:235-44. [PMID: 23856608 DOI: 10.1016/j.jprot.2013.06.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/11/2013] [Accepted: 06/29/2013] [Indexed: 12/25/2022]
Abstract
UNLABELLED Secreted proteins of bacteria are preferentially capable of interacting with host cells and are therefore of special biological and medical interest. Narrow pH range 2-DE and MALDI-TOFTOF-MS combine high-resolution protein separation with highly sensitive identification of proteins. Secreted proteins of Mycobacterium tuberculosis were separated at the protein species level, distinguishing different protein species of one protein. We focused on the pI range 4.0-4.7 and the Mr range 6-20kDa of the 2-DE pattern. Out of 128 analyzed spots, 121 were identified resulting in 33 different proteins with 277 different protein species, accumulating in a mean of 8.4 protein species per protein. Overrepresentation was found for the protein classes "virulence, detoxification, adaption", "information pathways", "cell wall and cell processes" and "intermediary metabolism and respiration". Thus far, 15 protein species of the ESX-1 family are characterized with 100% sequence coverage. More automated 2-DE procedures and more sensitive identification techniques are required for complete characterization of all of the protein species even in highly enriched samples, such as culture filtrates. Only then the functional level of proteomics will be achieved and potential biomarkers can be postulated at the molecular level. BIOLOGICAL SIGNIFICANCE Proteomics is dominated by bottom-up approaches largely ignoring protein speciation. A prerequisite to reach the protein species level is to obtain 100% sequence coverage, which is a major challenge in proteomics. Here we show complete sequence information with a 2-DE-MS approach for 15 protein species. Acetylation of the N-terminus of ESAT-6 inhibits interaction with CFP-10, with direct consequences for pathogen-host interaction. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Sabine Lange
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany
| | - Ida Rosenkrands
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Peter Andersen
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Department of Immunology, Berlin, Germany
| | - Peter R Jungblut
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany.
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Holland C, Schmid M, Zimny-Arndt U, Rohloff J, Stein R, Jungblut PR, Meyer TF. Quantitative phosphoproteomics reveals link between Helicobacter pylori infection and RNA splicing modulation in host cells. Proteomics 2011; 11:2798-811. [DOI: 10.1002/pmic.201000793] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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3
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Roeser J, Bischoff R, Bruins AP, Permentier HP. Oxidative protein labeling in mass-spectrometry-based proteomics. Anal Bioanal Chem 2010; 397:3441-55. [PMID: 20155254 PMCID: PMC2911539 DOI: 10.1007/s00216-010-3471-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 01/07/2023]
Abstract
Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)-mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.
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Affiliation(s)
- Julien Roeser
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Andries P. Bruins
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar P. Permentier
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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4
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Jungblut PR, Schiele F, Zimny-Arndt U, Ackermann R, Schmid M, Lange S, Stein R, Pleissner KP. Helicobacter pylori proteomics by 2-DE/MS, 1-DE-LC/MS and functional data mining. Proteomics 2010; 10:182-93. [PMID: 19941309 DOI: 10.1002/pmic.200900361] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
With its predicted proteome of 1550 proteins (data set Etalon) Helicobacter pylori 26695 represents a perfect model system of medium complexity for investigating basic questions in proteomics. We analyzed urea-solubilized proteins by 2-DE/MS (data set 2-DE) and by 1-DE-LC/MS (Supprot); proteins insoluble in 9 M urea but solubilized by SDS (Pellet); proteins precipitating in the Sephadex layer at the application side of IEF (Sephadex) by 1-DE-LC/MS; and proteins precipitating close to the application side within the IEF gel by LC/MS (Startline). The experimental proteomics data of H. pylori comprising 567 proteins (protein coverage: 36.6%) were stored in the Proteome Database System for Microbial Research (http://www.mpiib-berlin.mpg.de/2D-PAGE/), which gives access to raw mass spectra (MALDI-TOF/TOF) in T2D format, as well as to text files of peak lists. For data mining the protein mapping and comparison tool PROMPT (http://webclu.bio.wzw.tum.de/prompt/) was used. The percentage of proteins with transmembrane regions, relative to all proteins detected, was 0, 0.2, 0, 0.5, 3.8 and 6.3% for 2-DE, Supprot, Startline, Sephadex, Pellet, and Etalon, respectively. 2-DE does not separate membrane proteins because they are insoluble in 9 M urea/70 mM DTT and 2% CHAPS. SDS solubilizes a considerable portion of the urea-insoluble proteins and makes them accessible for separation by SDS-PAGE and LC. The 2-DE/MS analysis with urea-solubilized proteins and the 1-DE-LC/MS analysis with the urea-insoluble protein fraction (Pellet) are complementary procedures in the pursuit of a complete proteome analysis. Access to the PROMPT-generated diagrams in the Proteome Database allows the mining of experimental data with respect to other functional aspects.
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Affiliation(s)
- Peter R Jungblut
- Core Facility Protein Analysis, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.
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5
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Urban CF, Ermert D, Schmid M, Abu-Abed U, Goosmann C, Nacken W, Brinkmann V, Jungblut PR, Zychlinsky A. Neutrophil extracellular traps contain calprotectin, a cytosolic protein complex involved in host defense against Candida albicans. PLoS Pathog 2009; 5:e1000639. [PMID: 19876394 PMCID: PMC2763347 DOI: 10.1371/journal.ppat.1000639] [Citation(s) in RCA: 1206] [Impact Index Per Article: 80.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 09/30/2009] [Indexed: 02/07/2023] Open
Abstract
Neutrophils are the first line of defense at the site of an infection. They encounter and kill microbes intracellularly upon phagocytosis or extracellularly by degranulation of antimicrobial proteins and the release of Neutrophil Extracellular Traps (NETs). NETs were shown to ensnare and kill microbes. However, their complete protein composition and the antimicrobial mechanism are not well understood. Using a proteomic approach, we identified 24 NET-associated proteins. Quantitative analysis of these proteins and high resolution electron microscopy showed that NETs consist of modified nucleosomes and a stringent selection of other proteins. In contrast to previous results, we found several NET proteins that are cytoplasmic in unstimulated neutrophils. We demonstrated that of those proteins, the antimicrobial heterodimer calprotectin is released in NETs as the major antifungal component. Absence of calprotectin in NETs resulted in complete loss of antifungal activity in vitro. Analysis of three different Candida albicans in vivo infection models indicated that NET formation is a hitherto unrecognized route of calprotectin release. By comparing wild-type and calprotectin-deficient animals we found that calprotectin is crucial for the clearance of infection. Taken together, the present investigations confirmed the antifungal activity of calprotectin in vitro and, moreover, demonstrated that it contributes to effective host defense against C. albicans in vivo. We showed for the first time that a proportion of calprotectin is bound to NETs in vitro and in vivo.
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Affiliation(s)
- Constantin F. Urban
- Department for Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - David Ermert
- Department for Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Monika Schmid
- Protein Analysis Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Ulrike Abu-Abed
- Department for Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
- Microscopy Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Christian Goosmann
- Department for Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
- Microscopy Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Wolfgang Nacken
- Institute for Immunology, Münster University, Münster, Germany
- Institute for Molecular Virology, Center for Molecular Biology of Inflammation, Münster University, Münster, Germany
| | - Volker Brinkmann
- Microscopy Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Peter R. Jungblut
- Protein Analysis Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Arturo Zychlinsky
- Department for Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail:
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Zimny-Arndt U, Schmid M, Ackermann R, Jungblut PR. Classical proteomics: two-dimensional electrophoresis/MALDI mass spectrometry. Methods Mol Biol 2009; 492:65-91. [PMID: 19241027 DOI: 10.1007/978-1-59745-493-3_4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The rapid development in proteomics over the last 10 years has led to a series of new technologies and combinations of them designed to unravel as much as possible of the proteins of an organism or otherwise specified biological material. Despite being a little tricky at certain steps, 2-DE has a very high resolution power with more than 10,000 spots per gel and is able to separate one protein into its different protein species caused by posttranslational modifications, alternative splicing or genetic variability. This high-resolution separation is combined with a highly sensitive identification method using peptide mass fingerprinting combined with sequence information by MS/MS, which results in high sequence coverage: the key to elucidate protein species structures. The off-line measurement by MALDI-TOFTOF-MS allows the repeated measurement of each sample and therefore provides more complete structure information for each protein species. The presented protocols represent the basic technology consisting of 2-DE, two staining methods, tryptic digestion and MALDI-TOFTOF-MS.
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Galkin A, Meyer B, Wittig I, Karas M, Schägger H, Vinogradov A, Brandt U. Identification of the mitochondrial ND3 subunit as a structural component involved in the active/deactive enzyme transition of respiratory complex I. J Biol Chem 2008; 283:20907-13. [PMID: 18502755 PMCID: PMC2475694 DOI: 10.1074/jbc.m803190200] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 05/23/2008] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) undergoes reversible deactivation upon incubation at 30-37 degrees C. The active/deactive transition could play an important role in the regulation of complex I activity. It has been suggested recently that complex I may become modified by S-nitrosation under pathological conditions during hypoxia or when the nitric oxide:oxygen ratio increases. Apparently, a specific cysteine becomes accessible to chemical modification only in the deactive form of the enzyme. By selective fluorescence labeling and proteomic analysis, we have identified this residue as cysteine-39 of the mitochondrially encoded ND3 subunit of bovine heart mitochondria. Cysteine-39 is located in a loop connecting the first and second transmembrane helix of this highly hydrophobic subunit. We propose that this loop connects the ND3 subunit of the membrane arm with the PSST subunit of the peripheral arm of complex I, placing it in a region that is known to be critical for the catalytic mechanism of complex I. In fact, mutations in three positions of the loop were previously reported to cause Leigh syndrome with and without dystonia or progressive mitochondrial disease.
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Affiliation(s)
- Alexander Galkin
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
| | - Björn Meyer
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
| | - Ilka Wittig
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
| | - Michael Karas
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
| | - Hermann Schägger
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
| | - Andrei Vinogradov
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
| | - Ulrich Brandt
- Molecular Bioenergetics Group, Cluster of
Excellence Frankfurt “Macromolecular complexes,” Medical School,
Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, D-60590
Frankfurt am Main, Germany, the Institut
für Pharmazeutische Chemie, Cluster of Excellence Frankfurt
“Macromolecular complexes,” Johann Wolfgang
Goethe-Universität, Max-von-Laue Str.-9, D-60438 Frankfurt am Main,
Germany, and the Department of Biochemistry,
School of Biology, Moscow State University, Moscow 119992, Russian
Federation
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Paape D, Lippuner C, Schmid M, Ackermann R, Barrios-Llerena ME, Zimny-Arndt U, Brinkmann V, Arndt B, Pleissner KP, Jungblut PR, Aebischer T. Transgenic, fluorescent Leishmania mexicana allow direct analysis of the proteome of intracellular amastigotes. Mol Cell Proteomics 2008; 7:1688-701. [PMID: 18474515 DOI: 10.1074/mcp.m700343-mcp200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Investigating the proteome of intracellular pathogens is often hampered by inadequate methodologies to purify the pathogen free of host cell material. This has also precluded direct proteome analysis of the intracellular, amastigote form of Leishmania spp., protozoan parasites that cause a spectrum of diseases that affect some 12 million patients worldwide. Here a method is presented that combines classic, isopycnic density centrifugation with fluorescent particle sorting for purification by exploiting transgenic, fluorescent parasites to allow direct proteome analysis of the purified organisms. By this approach the proteome of intracellular Leishmania mexicana amastigotes was compared with that of extracellular promastigotes that are transmitted by insect vectors. In total, 509 different proteins were identified by mass spectrometry and database search. This number corresponds to approximately 6% of gene products predicted from the reference genome of Leishmania major. Intracellular amastigotes synthesized significantly more proteins with basic pI and showed a greater abundance of enzymes of fatty acid catabolism, which may reflect their living in acidic habitats and metabolic adaptation to nutrient availability, respectively. Bioinformatics analyses of the genes corresponding to the protein data sets produced clear evidence for skewed codon usage and translational bias in these organisms. Moreover analysis of the subset of genes whose products were more abundant in amastigotes revealed characteristic sequence motifs in 3'-untranslated regions that have been linked to translational control elements. This suggests that proteome data sets may be used to identify regulatory elements in mRNAs. Last but not least, at 6% coverage the proteome identified all vaccine antigens tested to date. Thus, the present data set provides a valuable resource for selection of candidate vaccine antigens.
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Affiliation(s)
- Daniel Paape
- Institute of Immunology and Infection Research, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom
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Eravci M, Fuxius S, Broedel O, Weist S, Krause E, Stephanowitz H, Schluter H, Eravci S, Baumgartner A. The whereabouts of transmembrane proteins from rat brain synaptosomes during two-dimensional gel electrophoresis. Proteomics 2008; 8:1762-70. [DOI: 10.1002/pmic.200700193] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Klein E, DeBonis S, Thiede B, Skoufias DA, Kozielski F, Lebeau L. New chemical tools for investigating human mitotic kinesin Eg5. Bioorg Med Chem 2007; 15:6474-88. [PMID: 17587586 DOI: 10.1016/j.bmc.2007.06.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 05/24/2007] [Accepted: 06/05/2007] [Indexed: 10/23/2022]
Abstract
We have designed and synthesized a series of monastrol derivatives, an allosteric inhibitor of Eg5, a motor protein responsible for the formation and maintenance of the bipolar spindle in mitotic cells. Sterically demanding structural modifications have been introduced on the skeleton of the parent drug either via a multicomponent Biginelli reaction or a stepwise modification of monastrol. The ability of these compounds to inhibit Eg5 activity has been investigated using two in vitro steady-state ATPase assays (basal and microtubule-stimulated) as well as a cell-based assay. One compound in the series appeared more potent than monastrol by a fivefold factor. Three other compounds that were unable to inhibit Eg5 ATPase activity in vitro proved potent Eg5 inhibitors in the cell-based assay. The results obtained led to the identification of structure-activity relationships further used to design an affinity matrix that can be used for fast and efficient purification of Eg5 from crude lysate of eukaryotic cells.
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Affiliation(s)
- Emmanuel Klein
- Institut Gilbert-Laustriat, CNRS-Université Louis Pasteur, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
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Rison SCG, Mattow J, Jungblut PR, Stoker NG. Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2007; 153:521-528. [PMID: 17259624 PMCID: PMC2884946 DOI: 10.1099/mic.0.2006/001537-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Identification of protein translation start sites is largely a bioinformatics exercise, with relatively few confirmed by N-terminal sequencing. Translation start site determination is critical for defining both the protein sequence and the upstream DNA which may contain regulatory motifs. It is demonstrated here that translation start sites can be determined during routine protein identification, using MALDI-MS and MS/MS data to select the correct N-terminal sequence from a list of alternatives generated in silico. Applying the method to 13 proteins from Mycobacterium tuberculosis, 11 predicted translational start sites were confirmed, and two reassigned. The authors suggest that these data (be they confirmation or reassignments) are important for the annotation of both this genome and those of organisms with related genes. It was also shown that N-acetylation, reported to be rare in prokaryotes, was present in three of the 13 proteins (23 %), suggesting that in the mycobacteria this modification may be common, and an important regulator of protein function, although more proteins need to be analysed. This method can be performed with little or no additional experimental work during proteomics investigations.
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Affiliation(s)
| | - Jens Mattow
- Max-Planck-Institute for Infection Biology, Core Facility Protein Analysis, Campus Charité Mitte, Schumannstr. 21/22, D-10117 Berlin, Germany
| | - Peter R. Jungblut
- Max-Planck-Institute for Infection Biology, Core Facility Protein Analysis, Campus Charité Mitte, Schumannstr. 21/22, D-10117 Berlin, Germany
| | - Neil G. Stoker
- The Royal Veterinary College, Royal College Street, London NW1 0TU, UK
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