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Article: Application of mass spectrometry in proteomics.

Guerrera, Ida Chiara / Kleiner, Oliver

2005 Volume 25, Issue 1-2, Page(s) 71–93

Abstract: Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in ... ...

Abstract	Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.
MeSH term(s)	Affinity Labels/analysis ; Isotope Labeling/methods ; Mass Spectrometry/instrumentation ; Mass Spectrometry/methods ; Molecular Structure ; Protein Processing, Post-Translational ; Proteins/analysis ; Proteins/chemistry ; Proteome/analysis ; Proteome/chemistry ; Proteomics/instrumentation ; Proteomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Affinity Labels ; Proteins ; Proteome
Language	English
Publishing date	2005-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1007/s10540-005-2849-x
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Article: Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase

Kaiser, Gebhard / Kleiner, Oliver / Beisswenger, Christoph / Batschauer, Alfred

Planta. 2009 Aug., v. 230, no. 3

2009

Abstract: Ultraviolet-B (UV-B, 280-320 nm) radiation may have severe negative effects on plants including damage to their genetic information. UV protection and DNA-repair mechanisms have evolved to either avoid or repair such damage. Since autotrophic plants are ... ...

Abstract	Ultraviolet-B (UV-B, 280-320 nm) radiation may have severe negative effects on plants including damage to their genetic information. UV protection and DNA-repair mechanisms have evolved to either avoid or repair such damage. Since autotrophic plants are dependent on sunlight for their energy supply, an increase in the amount of UV-B reaching the earth's surface may affect the integrity of their genetic information if DNA damage is not repaired efficiently and rapidly. Here we show that overexpression of cyclobutane pyrimidine dimer (CPD) photolyase (EC 4.1.99.3) in Arabidopsis thaliana (L.), which catalyses the reversion of the major UV-B photoproduct in DNA (CPDs), strongly enhances the repair of CPDs and results in a moderate increase of biomass production under elevated UV-B.
Keywords	Arabidopsis thaliana ; DNA ; DNA damage ; DNA repair ; biomass production ; catalytic activity ; energy ; plant damage ; solar radiation ; ultraviolet radiation
Language	English
Dates of publication	2009-08
Size	p. 505-515.
Publisher	Springer-Verlag
Publishing place	Berlin/Heidelberg
Document type	Article
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935
ISSN (online)	1432-2048
ISSN	0032-0935
DOI	10.1007/s00425-009-0962-y
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Article: Increased confidence in large-scale phosphoproteomics data by complementary mass spectrometric techniques and matching of phosphopeptide data sets.

Alcolea, Maria P / Kleiner, Oliver / Cutillas, Pedro R

Journal of proteome research

2009 Volume 8, Issue 8, Page(s) 3808–3815

Abstract: Large-scale phosphoproteomics studies are of great interest due to their potential for the dissection of signaling pathways controlled by protein kinases. Recent advances in mass spectrometry (MS)-based phosphoproteomic techniques offer new opportunities ...

Abstract	Large-scale phosphoproteomics studies are of great interest due to their potential for the dissection of signaling pathways controlled by protein kinases. Recent advances in mass spectrometry (MS)-based phosphoproteomic techniques offer new opportunities to profile protein kinase activities in a comprehensive manner. However, this increasingly used approach still poses many analytical challenges. On one hand, high stringency criteria for phosphopeptide identification based on MS/MS data are needed in order to avoid false positives; however, on the other hand, these stringent criteria also result in the introduction of many false negatives. In the current report, we employ different mass spectrometric techniques for large-scale phosphoproteomics in order to reduce the presence of false negatives and enhance data confidence. A LTQ-Orbitrap LC-MS/MS platform identified approximately 3 times more phosphopeptides than Q-TOF LC-MS/MS instrumentation (4308 versus 1485 identifications, respectively). In both cases, collision induced dissociation (CID) was used to fragment peptides. Interestingly, the two platforms produced complementary data as many of the low scoring phosphopeptide ions identified by LTQ-Orbitrap MS/MS gave rise to high score identifications by Q-TOF MS/MS analysis, and vice versa. In fact, approximately 450 phosphopeptides identified by the Q-TOF instrument were not identified by the LTQ-Orbitrap. Further data comparison revealed the extent of the problem: in one experiment, the estimated number of false negatives (1066) was close to the number of identified phosphopeptides (1485). This work demonstrates that by using standard procedures for phosphopeptide identification the number of false negatives can be even greater than the number of false positives. We propose using historical phosphoproteomic data and spectral matching algorithms in order to efficiently minimize false negative rates.
MeSH term(s)	Animals ; Chromatography, Liquid/methods ; Data Interpretation, Statistical ; Databases, Protein ; Mice ; NIH 3T3 Cells ; Phosphoproteins/analysis ; Proteomics/methods ; Reproducibility of Results ; Tandem Mass Spectrometry/methods
Chemical Substances	Phosphoproteins
Language	English
Publishing date	2009-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3893
ISSN	1535-3893
DOI	10.1021/pr800955n
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Article ; Online: Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase.

Kaiser, Gebhard / Kleiner, Oliver / Beisswenger, Christoph / Batschauer, Alfred

Planta

2009 Volume 230, Issue 3, Page(s) 505–515

Abstract	Ultraviolet-B (UV-B, 280-320 nm) radiation may have severe negative effects on plants including damage to their genetic information. UV protection and DNA-repair mechanisms have evolved to either avoid or repair such damage. Since autotrophic plants are dependent on sunlight for their energy supply, an increase in the amount of UV-B reaching the earth's surface may affect the integrity of their genetic information if DNA damage is not repaired efficiently and rapidly. Here we show that overexpression of cyclobutane pyrimidine dimer (CPD) photolyase (EC 4.1.99.3) in Arabidopsis thaliana (L.), which catalyses the reversion of the major UV-B photoproduct in DNA (CPDs), strongly enhances the repair of CPDs and results in a moderate increase of biomass production under elevated UV-B.
MeSH term(s)	Arabidopsis/enzymology ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Base Sequence ; DNA Primers ; DNA Repair ; Deoxyribodipyrimidine Photo-Lyase/genetics ; Plants, Genetically Modified ; Ultraviolet Rays
Chemical Substances	Arabidopsis Proteins ; DNA Primers ; Deoxyribodipyrimidine Photo-Lyase (EC 4.1.99.3)
Language	English
Publishing date	2009-06-12
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-009-0962-y
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Article ; Online: Evaluation of Pharmacokinetics and Pharmacodynamics of BI 425809, a Novel GlyT1 Inhibitor: Translational Studies.

Rosenbrock, Holger / Desch, Michael / Kleiner, Oliver / Dorner-Ciossek, Cornelia / Schmid, Bernhard / Keller, Sascha / Schlecker, Christina / Moschetti, Viktoria / Goetz, Sophia / Liesenfeld, Karl-Heinz / Fillon, Gwenaelle / Giovannini, Riccardo / Ramael, Steven / Wunderlich, Glen / Wind, Sven

Clinical and translational science

2018 Volume 11, Issue 6, Page(s) 616–623

Abstract: BI 425809 is a potent and selective glycine transporter 1 (GlyT1) inhibitor being developed for the treatment of cognitive impairment in Alzheimer disease and schizophrenia. Translational studies evaluated the effects of BI 425809 on glycine levels in ... ...

Abstract	BI 425809 is a potent and selective glycine transporter 1 (GlyT1) inhibitor being developed for the treatment of cognitive impairment in Alzheimer disease and schizophrenia. Translational studies evaluated the effects of BI 425809 on glycine levels in rat and human cerebrospinal fluid (CSF). Oral administration of BI 425809 in rats induced a dose-dependent increase of glycine CSF levels from 30% (0.2 mg/kg, not significant) to 78% (2 mg/kg, P < 0.01), relative to vehicle. Similarly, oral administration of BI 425809 in healthy volunteers resulted in a dose-dependent increase in glycine CSF levels at steady state, with a mean 50% increase at doses as low as 10 mg. The peak plasma concentration (C
MeSH term(s)	Administration, Oral ; Adult ; Alzheimer Disease/drug therapy ; Animals ; Area Under Curve ; Cell Line ; Dose-Response Relationship, Drug ; Glycine/cerebrospinal fluid ; Glycine/metabolism ; Glycine Plasma Membrane Transport Proteins/antagonists & inhibitors ; Glycine Plasma Membrane Transport Proteins/metabolism ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; Neurons ; Nootropic Agents/pharmacokinetics ; Nootropic Agents/pharmacology ; Nootropic Agents/therapeutic use ; Organic Chemicals/administration & dosage ; Organic Chemicals/pharmacokinetics ; Organic Chemicals/pharmacology ; Primary Cell Culture ; Rats ; Rats, Wistar ; Schizophrenia/drug therapy ; Young Adult
Chemical Substances	BI 425809 ; Glycine Plasma Membrane Transport Proteins ; Nootropic Agents ; Organic Chemicals ; SLC6A9 protein, human ; Slc6a9 protein, rat ; Glycine (TE7660XO1C)
Language	English
Publishing date	2018-08-23
Publishing country	United States
Document type	Clinical Trial, Phase I ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2433157-0
ISSN	1752-8062 ; 1752-8054
ISSN (online)	1752-8062
ISSN	1752-8054
DOI	10.1111/cts.12578
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Article ; Online: Psoriatic skin molecular and histopathologic profiles after treatment with risankizumab versus ustekinumab.

Visvanathan, Sudha / Baum, Patrick / Vinisko, Richard / Schmid, Ramona / Flack, Mary / Lalovic, Bojan / Kleiner, Oliver / Fuentes-Duculan, Judilyn / Garcet, Sandra / Davis, Justin W / Grebe, Kristie M / Fine, Jay S / Padula, Steven J / Krueger, James G

The Journal of allergy and clinical immunology

2018 Volume 143, Issue 6, Page(s) 2158–2169

Abstract: Background: IL-23 contributes to the activation, maintenance, and proliferation of T: Objective: We investigated the similarities and differences in molecular and histopathologic profiles in skin lesions from patients with psoriasis receiving ... ...

Abstract	Background: IL-23 contributes to the activation, maintenance, and proliferation of T Objective: We investigated the similarities and differences in molecular and histopathologic profiles in skin lesions from patients with psoriasis receiving risankizumab versus ustekinumab at an early time point. Methods: Lesional skin biopsy samples from 81 patients with moderate-to-severe plaque psoriasis participating in 2 different studies (a phase I risankizumab study and a phase II study of risankizumab vs ustekinumab) were analyzed by using histopathology, immunohistochemistry, and RNA sequencing. Results: Risankizumab induced a rapid decrease in levels of proteins and transcriptomic biomarkers associated with the IL-23 pathway, which were maintained through 8 weeks. At week 4, risankizumab decreased histopathologic expression of biomarkers, including K16, Ki67, CD3, lipocalin-2, CD11c, dendritic cell lysosome-associated membrane glycoprotein, β-defensin 2, and S100A7; global histopathologic scoring revealed that 54% and 69% of patients treated with 90 or 180 mg of risankizumab, respectively, were graded as experiencing "excellent improvement" versus 29% of patients treated with ustekinumab. At week 4, there was a common decrease in expression of 2645 genes expressed in lesional skin between patients receiving risankizumab and ustekinumab and a significant decrease in 2682 genes unique to risankizumab treatment. Risankizumab more strongly downregulated expression of genes associated with keratinocytes, epidermal cells, and monocytes, versus ustekinumab. Conclusion: Risankizumab demonstrated more pronounced changes in the molecular and histopathologic profile of psoriatic skin lesions compared with ustekinumab at week 4.
MeSH term(s)	Adult ; Antibodies, Monoclonal/therapeutic use ; Biopsy ; CD3 Complex/metabolism ; Down-Regulation ; Female ; Humans ; Immunohistochemistry ; Interleukin-12/antagonists & inhibitors ; Interleukin-23 Subunit p19/antagonists & inhibitors ; Ki-67 Antigen/metabolism ; Lipocalin-2/metabolism ; Lymphocyte Activation ; Male ; Middle Aged ; Psoriasis/drug therapy ; Psoriasis/pathology ; Sequence Analysis, RNA ; Skin/drug effects ; Skin/metabolism ; Skin/pathology ; Th17 Cells/immunology ; Treatment Outcome ; Ustekinumab/therapeutic use
Chemical Substances	Antibodies, Monoclonal ; CD3 Complex ; IL23A protein, human ; Interleukin-23 Subunit p19 ; Ki-67 Antigen ; Lipocalin-2 ; MKI67 protein, human ; Interleukin-12 (187348-17-0) ; risankizumab (90ZX3Q3FR7) ; Ustekinumab (FU77B4U5Z0)
Language	English
Publishing date	2018-12-20
Publishing country	United States
Document type	Clinical Trial, Phase I ; Comparative Study ; Journal Article ; Randomized Controlled Trial
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2018.11.042
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Article: Perspectives in spicing up proteomics with splicing.

Godovac-Zimmermann, Jasminka / Kleiner, Oliver / Brown, Larry R / Drukier, Andrzej K

Proteomics

2005 Volume 5, Issue 3, Page(s) 699–709

Abstract: In the post-genomics era there has been an acceleration of understanding of cellular and organismal biology and this acceleration has moved the goalposts for proteomics. Higher eukaryotes use alternative promoters, alternative splicing, RNA editing and ... ...

Abstract	In the post-genomics era there has been an acceleration of understanding of cellular and organismal biology and this acceleration has moved the goalposts for proteomics. Higher eukaryotes use alternative promoters, alternative splicing, RNA editing and post-translational modification to produce multiple isoforms of proteins from single genes. Switching amongst these isoforms is a major mechanism for control of cellular function. At present fundamental limitations in sensitivity, in absolute quantitation of proteins and in the characterization of protein structure at functionally important levels strongly limit the applicability of proteomics to higher eukaryotes. Recent developments suggest that quantitative, top-down proteomics analyses of complete proteins at sub-attomole levels are necessary for physiologically relevant studies of higher eukaryotes. New proteomics technologies which will ensure the future of proteomics as an important technology in medicine and cellular biology of higher eukaryotes are becoming available.
MeSH term(s)	Alternative Splicing ; Animals ; Humans ; Mass Spectrometry ; Protein Isoforms/metabolism ; Protein Splicing ; Protein Transport/physiology ; Proteome/analysis ; Sensitivity and Specificity
Chemical Substances	Protein Isoforms ; Proteome
Language	English
Publishing date	2005-02
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.200401051
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Article: Enrichment of phosphoproteins for proteomic analysis using immobilized Fe(III)-affinity adsorption chromatography.

Guerrera, Ida Chiara / Predic-Atkinson, Jelena / Kleiner, Oliver / Soskic, Vukic / Godovac-Zimmermann, Jasminka

Journal of proteome research

2005 Volume 4, Issue 5, Page(s) 1545–1553

Abstract: We described an efficient protocol to strongly enrich phosphoproteins from mixtures of total cellular proteins using homemade, recyclable Fe(III)-affinity columns. An integral feature of the method is the use of a detergent cocktail that allows use of ... ...

Abstract	We described an efficient protocol to strongly enrich phosphoproteins from mixtures of total cellular proteins using homemade, recyclable Fe(III)-affinity columns. An integral feature of the method is the use of a detergent cocktail that allows use of different pHs for total protein extraction (pH 6.8) and for subsequent affinity capture of phosphoproteins (pH 3.4). Affinity captured proteins from rat fibroblasts were fractionated on 2D gels and random selection was identified by mass spectrometry. More than 85% of identified proteins were previously known to be phosphorylated. The specificity of the method was further validated by isolating proteins from (32)P labeled cells. Our comparison of the clusters of acidic residues in the captured proteins with acidic clusters in proteins of the rat genome indicates that affinity for phosphate groups dominates over adsorption of proteins with acidic clusters.
MeSH term(s)	Adsorption ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Blotting, Western ; Chromatography, Affinity/methods ; Electrophoresis, Gel, Two-Dimensional ; Fibroblasts/metabolism ; Genome ; Hydrogen-Ion Concentration ; Iron/chemistry ; Kidney/metabolism ; Mass Spectrometry ; Molecular Sequence Data ; Phosphoproteins/chemistry ; Phosphorylation ; Protein Binding ; Protein Processing, Post-Translational ; Proteins/chemistry ; Proteomics/methods ; Rats ; Sequence Homology, Amino Acid ; Signal Transduction ; Silver Staining
Chemical Substances	Phosphoproteins ; Proteins ; Iron (E1UOL152H7)
Language	English
Publishing date	2005-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3893
ISSN	1535-3893
DOI	10.1021/pr050098m
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Article: Amphiphysin I phosphorylation on residue threonine 260 in a pentylenetetrazole-induced seizure model.

Choudhury, Mowdood / Kleiner, Oliver / Chung, Raymond / Barden, Laura / Morgan, Louise / Patel, Toshal R / Staddon, James M

Neuroscience letters

2008 Volume 444, Issue 3, Page(s) 245–249

Abstract: A method to evaluate kinase inhibitor action was reported [L. Morgan, S.J. Neame, H. Child, R. Chung, B. Shah, L. Barden, J.M. Staddon, T.R. Patel, Development of a pentylenetetrazole-induced seizure model to evaluate kinase inhibitor efficacy in the ... ...

Abstract	A method to evaluate kinase inhibitor action was reported [L. Morgan, S.J. Neame, H. Child, R. Chung, B. Shah, L. Barden, J.M. Staddon, T.R. Patel, Development of a pentylenetetrazole-induced seizure model to evaluate kinase inhibitor efficacy in the central nervous system, Neurosci. Lett. 395 (2006) 143-148]. In this, acute administration of the GABA antagonist pentylenetetrazole triggers seizures through glutamate-dependent pathways. Under such conditions, activation of the c-Jun N-terminal kinase (JNK) pathway was detected in hippocampal extracts. Phosphorylation of the upstream JNK kinase MKK4 was also revealed through use of a phospho-MKK4-specific antibody. Here, this antibody is shown to also react with a protein of approximately 125 kDa which underwent increased phosphorylation in response to pentylenetetrazole treatment. The present study aimed to identify the approximately 125 kDa protein as it may provide novel insight into signalling, neuronal activity and seizures. Using chromatographic methods and mass spectrometry, the protein was identified as amphiphysin I. This was confirmed by 2D gel analysis and immunoblot with amphiphysin I-specific antibodies. Although the phospho-MKK4 antibody was raised against an MKK4-specific peptide, partial sequence homology between this sequence and a region of amphiphysin was discerned. New antibodies raised against the phospho-threonine 260-amphiphysin-specific sequence detected increased phosphorylation in response to pentylenetetrazole treatment. This particular phosphorylation site does not seem to have been described before, possibly reflecting a novel regulatory aspect of amphiphysin biology. As amphiphysin is involved in the regulation of endocytosis, phosphorylation at this site may play a role in the regulated re-uptake of synaptic vesicles after neurotransmitter release.
MeSH term(s)	Animals ; GABA Antagonists ; Hippocampus/metabolism ; MAP Kinase Kinase 4/metabolism ; Mice ; Nerve Tissue Proteins/metabolism ; Pentylenetetrazole ; Phosphorylation ; Seizures/chemically induced ; Seizures/metabolism ; Threonine/metabolism
Chemical Substances	GABA Antagonists ; Nerve Tissue Proteins ; amphiphysin (147954-52-7) ; Threonine (2ZD004190S) ; MAP Kinase Kinase 4 (EC 2.7.12.2) ; Pentylenetetrazole (WM5Z385K7T)
Language	English
Publishing date	2008-10-31
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	194929-9
ISSN	1872-7972 ; 0304-3940
ISSN (online)	1872-7972
ISSN	0304-3940
DOI	10.1016/j.neulet.2008.08.055
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Article: Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity.

Kundu, Lal Mohan / Burgdorf, Lars T / Kleiner, Oliver / Batschauer, Alfred / Carell, Thomas

Chembiochem : a European journal of chemical biology

2002 Volume 3, Issue 11, Page(s) 1053–1060

Abstract: In order to gain deeper insight into the function and interplay of proteins in cells it is essential to develop methods that allow the profiling of protein function in real time, in solution, in cells, and in cell organelles. Here we report the ... ...

Abstract	In order to gain deeper insight into the function and interplay of proteins in cells it is essential to develop methods that allow the profiling of protein function in real time, in solution, in cells, and in cell organelles. Here we report the development of a U-type oligonucleotide (molecular beacon) that contains a fluorophore and a quencher at the tips, and in addition a substrate analogue in the loop structure. This substrate analogue induces a hairpin cleavage in response to enzyme action, which is translated into a fluorescence signal. The molecular beacon developed here was used to characterize DNA-photolyase activity. These enzymes represent a challenge for analytical methods because of their low abundance in cells. The molecular beacon made it possible to measure the activity of purified class I and class II photolyases. Photolyase activity was even detectable in crude cell extracts.
MeSH term(s)	DNA Repair ; Deoxyribodipyrimidine Photo-Lyase/metabolism ; Molecular Probes/chemical synthesis ; Nucleic Acid Conformation ; Oligonucleotides/chemical synthesis
Chemical Substances	Molecular Probes ; Oligonucleotides ; Deoxyribodipyrimidine Photo-Lyase (EC 4.1.99.3)
Language	English
Publishing date	2002-11-04
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/1439-7633(20021104)3:11<1053::AID-CBIC1053>3.0.CO;2-#
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