151
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de Graaf EL, Giansanti P, Altelaar AFM, Heck AJR. Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution. Mol Cell Proteomics 2014; 13:2426-34. [PMID: 24850871 DOI: 10.1074/mcp.o113.036608] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Quantitative phosphoproteomics workflows traditionally involve additional sample labeling and fractionation steps for accurate and in-depth analysis. Here we report a high-throughput, straightforward, and comprehensive label-free phosphoproteomics approach using the highly selective, reproducible, and sensitive Ti(4+)-IMAC phosphopeptide enrichment method. We demonstrate the applicability of this approach by monitoring the phosphoproteome dynamics of Jurkat T cells stimulated by prostaglandin E2 (PGE2) over six different time points, measuring in total 108 snapshots of the phosphoproteome. In total, we quantitatively monitored 12,799 unique phosphosites over all time points with very high quantitative reproducibility (average r > 0.9 over 100 measurements and a median cv < 0.2). PGE2 is known to increase cellular cAMP levels, thereby activating PKA. The in-depth analysis revealed temporal regulation of a wide variety of phosphosites associated not only with PKA, but also with a variety of other classes of kinases. Following PGE2 stimulation, several pathways became only transiently activated, revealing that in-depth dynamic profiling requires techniques with high temporal resolution. Moreover, the large publicly available dataset provides a valuable resource for downstream PGE2 signaling dynamics in T cells, and cAMP-mediated signaling in particular. More generally, our method enables in-depth, quantitative, high-throughput phosphoproteome screening on any system, requiring very little sample, sample preparation, and analysis time.
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Affiliation(s)
- Erik L de Graaf
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Piero Giansanti
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - A F Maarten Altelaar
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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152
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Abstract
In recent years, de novo peptide sequencing from mass spectrometry data has developed as one of the major peptide identification methods with the emergence of new instruments and advanced computational methods. However, there are still limitations to this method; for example, the typically used spectrum graph model cannot represent all the information and relationships inherent in tandem mass spectra (MS/MS spectra). Here, we present a new method named NovoHCD which applies a spectrum graph model with multiple types of edges (called a multi-edge graph), and integrates into it amino acid combination (AAC) information and peptide tags. In addition, information on immonium ions observed particularly in higher-energy collisional dissociation (HCD) spectra is incorporated. Comparisons between NovoHCD and another successful de novo peptide sequencing method for HCD spectra, pNovo, were performed. Experiments were conducted on five HCD spectral datasets. Results show that NovoHCD outperforms pNovo in terms of full length peptide identification accuracy; specifically, the accuracy increases 13%-21% over the five datasets.
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153
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Meyer JG. In Silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage. ISRN COMPUTATIONAL BIOLOGY 2014; 2014:960902. [PMID: 30687733 PMCID: PMC6347401 DOI: 10.1155/2014/960902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the postgenome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome is digested into peptides that are identified followed by protein inference. Despite continuous improvements to all steps of the shotgun proteomics workflow, observed proteome coverage is often low; some proteins are identified by a single peptide sequence. Complete proteome sequence coverage would allow comprehensive characterization of RNA splicing variants and all posttranslational modifications, which would drastically improve the accuracy of biological models. There are many reasons for the sequence coverage deficit, but ultimately peptide length determines sequence observability. Peptides that are too short are lost because they match many protein sequences and their true origin is ambiguous. The maximum observable peptide length is determined by several analytical challenges. This paper explores computationally how peptide lengths produced from several common proteome digestion methods limit observable proteome coverage. Iterative proteome cleavage strategies are also explored. These simulations reveal that maximized proteome coverage can be achieved by use of an iterative digestion protocol involving multiple proteases and chemical cleavages that theoretically allow 92.9% proteome coverage.
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Affiliation(s)
- Jesse G Meyer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
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154
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Tu C, Li J, Sheng Q, Zhang M, Qu J. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data. J Proteome Res 2014; 13:2069-79. [PMID: 24635752 PMCID: PMC3993956 DOI: 10.1021/pr401206m] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Survey-scan-based label-free method
have shown no compelling benefit
over fragment ion (MS2)-based approaches when low-resolution mass
spectrometry (MS) was used, the growing prevalence of high-resolution
analyzers may have changed the game. This necessitates an updated,
comparative investigation of these approaches for data acquired by
high-resolution MS. Here, we compared survey scan-based (ion current,
IC) and MS2-based abundance features including spectral-count (SpC)
and MS2 total-ion-current (MS2-TIC), for quantitative analysis using
various high-resolution LC/MS data sets. Key discoveries include:
(i) study with seven different biological data sets revealed only
IC achieved high reproducibility for lower-abundance proteins; (ii)
evaluation with 5-replicate analyses of a yeast sample showed IC provided
much higher quantitative precision and lower missing data; (iii) IC,
SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range;
(iv)
both MS2-TIC and IC showed good linear response to various protein
loading amounts but not SpC; (v) quantification using a well-characterized
CPTAC data set showed that IC exhibited markedly higher quantitative
accuracy, higher sensitivity, and lower false-positives/false-negatives
than both SpC and MS2-TIC. Therefore, IC achieved an overall superior
performance than the MS2-based strategies in terms of reproducibility,
missing data, quantitative dynamic range, quantitative accuracy, and
biomarker discovery.
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Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York , Buffalo, NY 14260, United States
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155
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Pieles K, Glatter T, Harms A, Schmidt A, Dehio C. An experimental strategy for the identification of AMPylation targets from complex protein samples. Proteomics 2014; 14:1048-52. [PMID: 24677795 DOI: 10.1002/pmic.201300470] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/07/2014] [Accepted: 01/29/2014] [Indexed: 11/06/2022]
Abstract
AMPylation is a posttranslational modification (PTM) that has recently caught much attention in the context of bacterial infections as pathogens were shown to secrete Fic proteins that AMPylate Rho GTPases and thus interfere with host cell signaling processes. Although Fic proteins are widespread and found in all kingdoms of life, only a small number of AMPylation targets are known to date. A major obstacle to target identification is the limited availability of generic strategies allowing sensitive and robust identification of AMPylation events. Here, we present an unbiased MS-based approach utilizing stable isotope-labeled ATP. The ATP isotopes are transferred onto target proteins in crude cell lysates by in vitro AMPylation introducing specific reporter ion clusters that allow detection of AMPylated peptides in complex biological samples by MS analysis. Applying this strategy on the secreted Fic protein Bep2 of Bartonella rochalimae, we identified the filamenting protein vimentin as an AMPylation target that was confirmed by independent assays. Vimentin represents a new class of target proteins and its identification emphasizes our method as a valuable tool to systematically uncover AMPylation targets. Furthermore, the approach can be generically adapted to study targets of other PTMs that allow incorporation of isotopically labeled substrates.
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156
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D'Annibale S, Kim J, Magliozzi R, Low TY, Mohammed S, Heck AJR, Guardavaccaro D. Proteasome-dependent degradation of transcription factor activating enhancer-binding protein 4 (TFAP4) controls mitotic division. J Biol Chem 2014; 289:7730-7. [PMID: 24500709 PMCID: PMC3953283 DOI: 10.1074/jbc.m114.549535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 02/04/2014] [Indexed: 11/06/2022] Open
Abstract
TFAP4, a basic helix-loop-helix transcription factor that regulates the expression of a multitude of genes involved in the regulation of cellular proliferation, stemness, and epithelial-mesenchymal transition, is up-regulated in colorectal cancer and a number of other human malignancies. We have found that, during the G2 phase of the cell division cycle, TFAP4 is targeted for proteasome-dependent degradation by the SCF(βTrCP) ubiquitin ligase. This event requires phosphorylation of TFAP4 on a conserved degron. Expression of a stable TFAP4 mutant unable to interact with βTrCP results in a number of mitotic defects, including chromosome missegregation and multipolar spindles, which eventually lead to the activation of the DNA damage response. Our findings reveal that βTrCP-dependent degradation of TFAP4 is required for the fidelity of mitotic division.
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Affiliation(s)
- Sara D'Annibale
- From the Hubrecht Institute-KNAW and University Medical Center Utrecht
| | - Jihoon Kim
- From the Hubrecht Institute-KNAW and University Medical Center Utrecht
| | - Roberto Magliozzi
- From the Hubrecht Institute-KNAW and University Medical Center Utrecht
| | - Teck Yew Low
- the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and
- The Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and
- The Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and
- The Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
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157
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Cynthia Martin F, Hiller M, Spitali P, Oonk S, Dalebout H, Palmblad M, Chaouch A, Guglieri M, Straub V, Lochmüller H, Niks EH, Verschuuren JJGM, Aartsma‐Rus A, Deelder AM, Burgt YEM, 't Hoen PAC. Fibronectin is a serum biomarker for
D
uchenne muscular dystrophy. Proteomics Clin Appl 2014; 8:269-78. [DOI: 10.1002/prca.201300072] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/05/2013] [Accepted: 11/17/2013] [Indexed: 01/23/2023]
Affiliation(s)
- F. Cynthia Martin
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Monika Hiller
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Pietro Spitali
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Stijn Oonk
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Amina Chaouch
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Michela Guglieri
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Volker Straub
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Hanns Lochmüller
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Erik H. Niks
- Department of Neurology Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | | | - Annemieke Aartsma‐Rus
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - André M. Deelder
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Yuri E. M. Burgt
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Peter A. C. 't Hoen
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
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158
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Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD). Proc Natl Acad Sci U S A 2014; 111:4507-12. [PMID: 24616531 DOI: 10.1073/pnas.1321458111] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification of HLA class I-associated peptides. However, the HLA class I peptide repertoire remains largely unexplored because the variable nature of endogenous peptides represents difficulties in conventional peptide fragmentation technology. Here, we substantially enhanced (about threefold) the identification success rate of peptides presented by HLA class I using combined electron-transfer/higher-energy collision dissociation (EThcD), reporting over 12,000 high-confident (false discovery rate <1%) peptides from a single human B-cell line. The direct importance of such an unprecedented large dataset is highlighted by the discovery of unique features in antigen presentation. The observation that a substantial part of proteins is sampled across different HLA alleles, and the common occurrence of HLA class I nested sets, suggest that the constraints of HLA class I to comprehensively present the health states of cells are not as tight as previously thought. Our dataset contains a substantial set of peptides bearing a variety of posttranslational modifications presented with marked allele-specific differences. We propose that EThcD should become the method of choice in analyzing HLA class I-presented peptides.
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159
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Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T. Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. MOLECULAR BIOSYSTEMS 2014; 9:2231-47. [PMID: 23748837 DOI: 10.1039/c3mb00009e] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.
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Affiliation(s)
- Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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160
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Nandakumar R, Talapatra K. Quantitative profiling of bacteriocins present in dairy-free probiotic preparations of Lactobacillus acidophilus by nanoliquid chromatography-tandem mass spectrometry. J Dairy Sci 2014; 97:1999-2008. [PMID: 24565320 DOI: 10.3168/jds.2013-7470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 12/28/2013] [Indexed: 01/22/2023]
Abstract
Bacteriocins are a heterogeneous group of ribosomally synthesized peptides or proteins with antimicrobial activity, produced predominantly by lactic acid bacteria, with potential applications as biopreservatives and probiotics. We describe here a novel strategy based on a bottom-up, shotgun proteomic approach using nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) with multiple fragmentation techniques for the quantitative profiling of bacteriocins present in the probiotic preparations of Lactobacillus acidophilus. A direct LC-MS/MS analysis with alternate collision-induced dissociation, high-energy collision dissociation, and electron-transfer dissociation fragmentation following a filter-assisted size-exclusion sample prefractionation has resulted in the identification of peptides belonging to 37 bacteriocins or related proteins. Peptides from lactacin F, helveticin J, lysin, avicin A, acidocin M, curvaticin FS47, and carocin D were predominant. The process of freeze drying under vacuum was observed to affect both the diversity and abundance of bacteriocins. Data acquisition using alternating complementary peptide fragmentation modes, especially electron-transfer dissociation, has significantly enhanced the peptide sequence coverage and number of bacteriocin peptides identified. Multi-enzyme proteolytic digestion was observed to increase the sample complexity and dynamic range, lowering the chances of detection of low-abundant bacteriocin peptides by LC-MS/MS. An analytical platform integrating size exclusion prefractionation, nanoLC-MS/MS analysis with multiple fragmentation techniques, and data-dependent decision tree-driven bioinformatic data analysis is novel in bacteriocin research and suitable for the comprehensive bioanalysis of diverse, low-abundant bacteriocins in complex samples.
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Affiliation(s)
- Renu Nandakumar
- Proteomics and Metabolomics Core Facility, Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588.
| | - Kesh Talapatra
- Natren Inc., 2382 Townsgate Rd, Westlake Village, CA 91361
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161
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Corfe BM, Evans CA. Are proteins a redundant ontology? Epistemological limitations in the analysis of multistate species. MOLECULAR BIOSYSTEMS 2014; 10:1228-35. [PMID: 24531646 DOI: 10.1039/c3mb70558g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Advances in proteomics have exponentially increased the numbers of post-translational modifications identified, the resulting volume of data is overwhelming both databases and empiricists. We review methodologies for chemical and functional PTM assignment. Using β-oxidation as a paradigm, we discuss epistemic limitations and conceptual approaches to resolving them combining relational biology, proteomics, and the erosion of "protein" and "metabolite" as distinct ontologies.
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Affiliation(s)
- Bernard M Corfe
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology, University of Sheffield, UK.
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162
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Benevento M, Munoz J. Role of mass spectrometry-based proteomics in the study of cellular reprogramming and induced pluripotent stem cells. Expert Rev Proteomics 2014; 9:379-99. [DOI: 10.1586/epr.12.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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163
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Abstract
Top-down proteomics has become a popular approach for the analysis of intact proteins. The term "top down" has been coined for the analysis of proteins not involving any enzymatic or chemical cleavage but rather the ionization of the protein as a sound molecule and mass analysis of intact species and fragment ions thereof produced upon dissociation inside a mass spectrometer. One or several charge states of the protein are mass-isolated and subjected to dissociation (MS/MS) in the gas phase. The obtained fragment masses, predominantly from cleavages of the protein along its amino acid backbone, are directly related to the intact protein. Using bioinformatics tools the fragment masses are matched against a known protein sequence or can alternatively be used for partial or full de novo sequencing, depending on the size of the protein and the number of fragment ions obtained. Moreover, this approach provides global information about modification states of proteins including the number and types of isoforms and their stoichiometry and allows for the precise localization of modifications within the amino acid sequence. Top-down analysis of a single, purified protein can be performed by matrix-assisted laser desorption ionization or electrospray ionization upon direct infusion without online chromatographic separation, whereas top-down analysis of complex protein mixtures makes pre-fractionation combined with an efficient front-end chromatographic separation coupled online to the mass spectrometer inevitable.
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Affiliation(s)
- Kai Scheffler
- Thermo Fisher Scientific, Im Steingrund 4-6, 63303, Dreieich, Germany,
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164
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A review of electron-capture and electron-transfer dissociation tandem mass spectrometry in polymer chemistry. Anal Chim Acta 2014; 808:44-55. [DOI: 10.1016/j.aca.2013.09.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/03/2013] [Accepted: 09/18/2013] [Indexed: 01/24/2023]
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165
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Shuck SC, Rose KL, Marnett LJ. Mass spectrometric methods for the analysis of nucleoside-protein cross-links: application to oxopropenyl-deoxyadenosine. Chem Res Toxicol 2013; 27:136-46. [PMID: 24359270 DOI: 10.1021/tx400384e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrophilic DNA adducts produced following oxidative stress can form DNA-protein cross-links (DPCs), dramatically altering genomic maintenance pathways. Complete characterization of DPCs has been hindered, in part, because of a lack of comprehensive techniques for their analysis. We have, therefore, established a proteomics approach to investigate sites of cross-link formation using N(6)-(3-oxo-1-propenyl)-2'-deoxyadenosine (OPdA), an electrophilic DNA adduct produced from oxidative stress. OPdA was reacted with albumin and reduced with NaBH4 to stabilize DPCs. Using LC-MS/MS proteomics techniques, high-resolution peptide sequence data were obtained; however, using a database searching strategy, adducted peptides were only identified in samples subjected to chemical depurination. This strategy revealed multiple oxopropenyl adenine-lysine adducts and oxopropenyl-lysine adducts with the most reactive lysines identified to be Lys256 and Lys548. Manual interrogation of the mass spectral data provided evidence of OPdA deoxynucleoside conjugates to lysines and cross-links that underwent facile collision-induced dissociation to release an unmodified peptide without subsequent fragmentation. These fragmentations precluded adduct detection and peptide sequencing using database searching methods. Thus, comprehensive analysis of DPCs requires chemical depurination of DNA-protein reaction mixtures followed by a combination of database-dependent and manual interrogation of LC-MS/MS data using higher-energy collision-induced dissociation. In the present case, this approach revealed that OPdA selectively modifies surface lysine residues and produces nucleoside-protein cross-links and oxopropenyl lysine.
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Affiliation(s)
- Sarah C Shuck
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
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166
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Nicolardi S, Giera M, Kooijman P, Kraj A, Chervet JP, Deelder AM, van der Burgt YEM. On-line electrochemical reduction of disulfide bonds: improved FTICR-CID and -ETD coverage of oxytocin and hepcidin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1980-7. [PMID: 24018861 PMCID: PMC3837188 DOI: 10.1007/s13361-013-0725-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/25/2013] [Accepted: 07/25/2013] [Indexed: 05/21/2023]
Abstract
Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80% (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.
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Affiliation(s)
- Simone Nicolardi
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Martin Giera
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Pieter Kooijman
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | | | | | - André M. Deelder
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
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167
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Silva AMN, Vitorino R, Domingues MRM, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med 2013; 65:925-941. [PMID: 24002012 DOI: 10.1016/j.freeradbiomed.2013.08.184] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 12/14/2022]
Abstract
In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.
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Affiliation(s)
- André M N Silva
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7 ET, United Kingdom
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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Song C, Wang F, Cheng K, Wei X, Bian Y, Wang K, Tan Y, Wang H, Ye M, Zou H. Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy. J Proteome Res 2013; 13:241-8. [DOI: 10.1021/pr400544j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Chunxia Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- SINOPEC Research Institute of Petroleum Processing, 18 Xueyuan Road, Beijing 100083, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xiaoluan Wei
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yexiong Tan
- The
International Cooperation Laboratory on Signal Transduction of Eastern
Hepatobiliary Surgery Institute, Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
| | - Hongyang Wang
- The
International Cooperation Laboratory on Signal Transduction of Eastern
Hepatobiliary Surgery Institute, Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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169
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Pollo-Oliveira L, Post H, Acencio ML, Lemke N, van den Toorn H, Tragante V, Heck AJR, Altelaar AFM, Yatsuda AP. Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics. Parasit Vectors 2013; 6:335. [PMID: 24267406 PMCID: PMC4182915 DOI: 10.1186/1756-3305-6-335] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The apicomplexan parasite Neospora caninum causes neosporosis, a disease that leads to abortion or stillbirth in cattle, generating an economic impact on the dairy and beef cattle trade. As an obligatory intracellular parasite, N. caninum needs to invade the host cell in an active manner to survive. The increase in parasite cytosolic Ca2+ upon contact with the host cell mediates critical events, including the exocytosis of phylum-specific secretory organelles and the activation of the parasite invasion motor. Because invasion is considered a requirement for pathogen survival and replication within the host, the identification of secreted proteins (secretome) involved in invasion may be useful to reveal interesting targets for therapeutic intervention. METHODS To chart the currently missing N. caninum secretome, we employed mass spectrometry-based proteomics to identify proteins present in the N. caninum tachyzoite using two different approaches. The first approach was identifying the proteins present in the tachyzoite-secreted fraction (ESA). The second approach was determining the relative quantification through peptide stable isotope labelling of the tachyzoites submitted to an ethanol secretion stimulus (discharged tachyzoite), expecting to identify the secreted proteins among the down-regulated group. RESULTS As a result, 615 proteins were identified at ESA and 2,011 proteins quantified at the discharged tachyzoite. We have analysed the connection between the secreted and the down-regulated proteins and searched for putative regulators of the secretion process among the up-regulated proteins. An interaction network was built by computational prediction involving the up- and down-regulated proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD000424. CONCLUSIONS The comparison between the protein abundances in ESA and their measure in the discharged tachyzoite allowed for a more precise identification of the most likely secreted proteins. Information from the network interaction and up-regulated proteins was important to recognise key proteins potentially involved in the metabolic regulation of secretion. Our results may be helpful to guide the selection of targets to be investigated against Neospora caninum and other Apicomplexan organisms.
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Affiliation(s)
- Letícia Pollo-Oliveira
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto e Núcleo de Apoio à Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Universidade de São Paulo, Av do Café , s/n, Ribeirão Preto, SP 14040-903, Brazil
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - Marcio Luis Acencio
- Botucatu Institute of Biosciences, UNESP - Univ Estadual Paulista, Distrito de Rubião Jr, s/n, Botucatu, São Paulo 18918-970, Brazil
| | - Ney Lemke
- Botucatu Institute of Biosciences, UNESP - Univ Estadual Paulista, Distrito de Rubião Jr, s/n, Botucatu, São Paulo 18918-970, Brazil
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - Vinicius Tragante
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Albert JR Heck
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3884 CH, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, Utrecht 3884 CH, The Netherlands
| | - Ana Patrícia Yatsuda
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto e Núcleo de Apoio à Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Universidade de São Paulo, Av do Café , s/n, Ribeirão Preto, SP 14040-903, Brazil
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170
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Zheng J, Liu L, Wang J, Jin Q. Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy. BMC Genomics 2013; 14:777. [PMID: 24215720 PMCID: PMC3832905 DOI: 10.1186/1471-2164-14-777] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/28/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnant and non-pregnant patients using gel electrophoresis and high-resolution mass spectrometry. Furthermore, we also apply a non-prefractionation quantitative phosphoproteomic approach using mTRAQ labeling to evaluate the expression of specific phosphoproteins during pregnancy comparison with non-pregnancy. RESULTS In total, 2579 proteins (10429 unique peptides) were identified, including 1408 from the urine of pregnant volunteers and 1985 from the urine of non-pregnant volunteers. One thousand and twenty-three proteins were not reported in previous studies at the proteome level and were unique to our study. Furthermore, we obtained 237 phosphopeptides, representing 105 phosphoproteins. Among these phosphoproteins, 16 of them were found to be significantly differentially expressed, of which 14 were up-regulated and two were down-regulated in urine samples from women just before vaginal delivery. CONCLUSION Taken together, these results offer a comprehensive urinary proteomic profile of healthy women during before and after vaginal delivery and novel information on the phosphoproteins that are differentially regulated during the maintenance of normal pregnancy. Our results may provide a better understanding of the mechanisms of pregnancy maintenance, potentially leading to the development of biomarker-based sensitive assays for understanding pregnancy.
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Affiliation(s)
| | | | | | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No,6, Rongjing East Street, BDA, Beijing 100176, China.
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171
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Diedrich JK, Pinto AFM, Yates JR. Energy dependence of HCD on peptide fragmentation: stepped collisional energy finds the sweet spot. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1690-9. [PMID: 23963813 PMCID: PMC3815594 DOI: 10.1007/s13361-013-0709-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 06/30/2013] [Accepted: 07/06/2013] [Indexed: 05/10/2023]
Abstract
An understanding of the process of peptide fragmentation and what parameters are best to obtain the most useful information is important. This is especially true for large-scale proteomics where data collection and data analysis are most often automated, and manual interpretation of spectra is rare because of the vast amounts of data generated. We show herein that collisional cell peptide fragmentation, in this case higher collisional dissociation (HCD) in the Q Exactive, is significantly affected by the normalized energy applied. Both peptide sequence and energy applied determine what ion fragments are observed. However, by applying a stepped normalized collisional energy scheme and combining ions from low, medium, and high collision energies, we are able to increase the diversity of fragmentation ions generated. Application of stepped collision energy to HEK293T lysate demonstrated a minimal effect on peptide and protein identification in a large-scale proteomics dataset, but improved phospho site localization through increased sequence coverage. Stepped HCD is also beneficial for tandem mass tagged (TMT) experiments, increasing intensity of TMT reporters used for quantitation without adversely effecting peptide identification.
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Affiliation(s)
- Jolene K Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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172
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Frese CK, Nolting D, Altelaar AFM, Griep-Raming J, Mohammed S, Heck AJR. Characterization of electron transfer dissociation in the Orbitrap Velos HCD cell. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1663-1670. [PMID: 23605687 DOI: 10.1007/s13361-013-0618-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
Electron transfer dissociation (ETD) is commonly employed in ion traps utilizing rf fields that facilitate efficient electron transfer reactions. Here, we explore performing ETD in the HCD collision cell on an Orbitrap Velos instrument by applying a static DC gradient axially to the rods. This gradient enables simultaneous three dimensional, charge sign independent, trapping of cations and anions, initiating electron transfer reactions in the center of the HCD cell where oppositely charged ions clouds overlap. Here, we evaluate this mode of operation for a number of tryptic peptide populations and the top-down sequence analysis of ubiquitin. Our preliminary data show that performing ETD in the HCD cell provides similar fragmentation as ion trap-ETD but requires further optimization to match performance of ion trap-ETD.
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Affiliation(s)
- Christian K Frese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
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173
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Palaniappan KK, Hangauer MJ, Smith TJ, Smart BP, Pitcher AA, Cheng EH, Bertozzi CR, Boyce M. A chemical glycoproteomics platform reveals O-GlcNAcylation of mitochondrial voltage-dependent anion channel 2. Cell Rep 2013; 5:546-52. [PMID: 24120863 DOI: 10.1016/j.celrep.2013.08.048] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 07/21/2013] [Accepted: 08/30/2013] [Indexed: 12/13/2022] Open
Abstract
Protein modification by O-linked β-N-acetylglucosamine (O-GlcNAc) is a critical cell signaling modality, but identifying signal-specific O-GlcNAcylation events remains a significant experimental challenge. Here, we describe a method for visualizing and analyzing organelle- and stimulus-specific O-GlcNAcylated proteins and use it to identify the mitochondrial voltage-dependent anion channel 2 (VDAC2) as an O-GlcNAc substrate. VDAC2(-/-) cells resist the mitochondrial dysfunction and apoptosis caused by global O-GlcNAc perturbation, demonstrating a functional connection between O-GlcNAc signaling and mitochondrial physiology through VDAC2. More broadly, our method will enable the discovery of signal-specific O-GlcNAcylation events in a wide array of experimental contexts.
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174
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Hayakawa E, Menschaert G, De Bock PJ, Luyten W, Gevaert K, Baggerman G, Schoofs L. Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation. J Proteome Res 2013; 12:5410-21. [PMID: 24032530 DOI: 10.1021/pr400446z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom peptides, and antimicrobial peptides. Since these peptides are processed at sites that are difficult to predict reliably, the search of their MS/MS spectra in sequence databases needs to be done without any protease setting. In addition, many endogenous peptides carry various post-translational modifications, making it essential to take these into account in the database search. These characteristics of endogenous peptides result in a huge search space, frequently leading to poor confidence of the peptide characterizations in peptidomics studies. We have developed a new MS/MS spectrum search tool for highly accurate and confident identification of endogenous peptides by combining two different fragmentation methods. Our approach takes advantage of the combination of two independent fragmentation methods (collision-induced dissociation and electron transfer dissociation). Their peptide spectral matching is carried out separately in both methods, and the final score is built as a combination of the two separate scores. We demonstrate that this approach is very effective in discriminating correct peptide identifications from false hits. We applied this approach to a spectral data set of neuropeptides extracted from mouse pituitary tumor cells. Compared to conventional MS-based identification, i.e., using a single fragmentation method, our approach significantly increased the peptide identification rate. It proved also highly effective for scanning spectra against a very large search space, enabling more accurate genome-wide searches and searches including multiple potential post-translational modifications.
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Affiliation(s)
- Eisuke Hayakawa
- Research Group of Functional Genomics and Proteomics, KU Leuven , Leuven, Belgium
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175
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Di Palma S, Zoumaro-Djayoon A, Peng M, Post H, Preisinger C, Munoz J, Heck AJ. Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography. J Proteomics 2013; 91:331-7. [DOI: 10.1016/j.jprot.2013.07.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/07/2013] [Accepted: 07/22/2013] [Indexed: 10/26/2022]
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176
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Szymanski WG, Kierszniowska S, Schulze WX. Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures. J Vis Exp 2013:e50535. [PMID: 24121251 DOI: 10.3791/50535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plasma membrane microdomains are features based on the physical properties of the lipid and sterol environment and have particular roles in signaling processes. Extracting sterol-enriched membrane microdomains from plant cells for proteomic analysis is a difficult task mainly due to multiple preparation steps and sources for contaminations from other cellular compartments. The plasma membrane constitutes only about 5-20% of all the membranes in a plant cell, and therefore isolation of highly purified plasma membrane fraction is challenging. A frequently used method involves aqueous two-phase partitioning in polyethylene glycol and dextran, which yields plasma membrane vesicles with a purity of 95% (1). Sterol-rich membrane microdomains within the plasma membrane are insoluble upon treatment with cold nonionic detergents at alkaline pH. This detergent-resistant membrane fraction can be separated from the bulk plasma membrane by ultracentrifugation in a sucrose gradient (2). Subsequently, proteins can be extracted from the low density band of the sucrose gradient by methanol/chloroform precipitation. Extracted protein will then be trypsin digested, desalted and finally analyzed by LC-MS/MS. Our extraction protocol for sterol-rich microdomains is optimized for the preparation of clean detergent-resistant membrane fractions from Arabidopsis thaliana cell cultures. We use full metabolic labeling of Arabidopsis thaliana suspension cell cultures with K(15)NO3 as the only nitrogen source for quantitative comparative proteomic studies following biological treatment of interest (3). By mixing equal ratios of labeled and unlabeled cell cultures for joint protein extraction the influence of preparation steps on final quantitative result is kept at a minimum. Also loss of material during extraction will affect both control and treatment samples in the same way, and therefore the ratio of light and heave peptide will remain constant. In the proposed method either labeled or unlabeled cell culture undergoes a biological treatment, while the other serves as control (4).
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177
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Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, Coon JJ. Neutron-encoded signatures enable product ion annotation from tandem mass spectra. Mol Cell Proteomics 2013; 12:3812-23. [PMID: 24043425 DOI: 10.1074/mcp.m113.028951] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We report the use of neutron-encoded (NeuCode) stable isotope labeling of amino acids in cell culture for the purpose of C-terminal product ion annotation. Two NeuCode labeling isotopologues of lysine, (13)C6(15)N2 and (2)H8, which differ by 36 mDa, were metabolically embedded in a sample proteome, and the resultant labeled proteins were combined, digested, and analyzed via liquid chromatography and mass spectrometry. With MS/MS scan resolving powers of ~50,000 or higher, product ions containing the C terminus (i.e. lysine) appear as a doublet spaced by exactly 36 mDa, whereas N-terminal fragments exist as a single m/z peak. Through theory and experiment, we demonstrate that over 90% of all y-type product ions have detectable doublets. We report on an algorithm that can extract these neutron signatures with high sensitivity and specificity. In other words, of 15,503 y-type product ion peaks, the y-type ion identification algorithm correctly identified 14,552 (93.2%) based on detection of the NeuCode doublet; 6.8% were misclassified (i.e. other ion types that were assigned as y-type products). Searching NeuCode labeled yeast with PepNovo(+) resulted in a 34% increase in correct de novo identifications relative to searching through MS/MS only. We use this tool to simplify spectra prior to database searching, to sort unmatched tandem mass spectra for spectral richness, for correlation of co-fragmented ions to their parent precursor, and for de novo sequence identification.
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Affiliation(s)
- Alicia L Richards
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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178
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Engholm-Keller K, Larsen MR. Technologies and challenges in large-scale phosphoproteomics. Proteomics 2013; 13:910-31. [PMID: 23404676 DOI: 10.1002/pmic.201200484] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 12/23/2022]
Abstract
Phosphorylation, the reversible addition of a phosphate group to amino acid side chains of proteins, is a fundamental regulator of protein activity, stability, and molecular interactions. Most cellular processes, such as inter- and intracellular signaling, protein synthesis, degradation, and apoptosis, rely on phosphorylation. This PTM is thus involved in many diseases, rendering localization and assessment of extent of phosphorylation of major scientific interest. MS-based phosphoproteomics, which aims at describing all phosphorylation sites in a specific type of cell, tissue, or organism, has become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments with focus on the various challenges and limitations this field currently faces.
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Affiliation(s)
- Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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179
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Meijer LAT, Zhou H, Chan OYA, Altelaar AFM, Hennrich ML, Mohammed S, Bos JL, Heck AJR. Quantitative global phosphoproteomics of human umbilical vein endothelial cells after activation of the Rap signaling pathway. MOLECULAR BIOSYSTEMS 2013; 9:732-49. [PMID: 23403867 DOI: 10.1039/c3mb25524g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The small GTPase Rap1 is required for proper cell-cell junction formation and also plays a key role in mediating cAMP-induced tightening of adherens junctions and subsequent increased barrier function of endothelial cells. To further study how Rap1 controls barrier function, we performed quantitative global phosphoproteomics in human umbilical vein endothelial cells (HUVECs) prior to and after Rap1 activation by the Epac-selective cAMP analog 8-pCPT-2'-O-Me-cAMP-AM (007-AM). Tryptic digests were labeled using stable isotope dimethyl labeling, enriched with phosphopeptides by strong cation exchange (SCX), followed by titanium(iv) immobilized metal affinity chromatography (Ti(4+)-IMAC) and analyzed by high resolution mass spectrometry. We identified 19 859 unique phosphopeptides containing 17 278 unique phosphosites on 4594 phosphoproteins, providing the largest HUVEC phosphoproteome to date. Of all identified phosphosites, 220 (∼1%) were more than 1.5-fold up- or downregulated upon Rap activation, in two independent experiments. Compatible with the function of Rap1, these alterations were found predominantly in proteins regulating the actin cytoskeleton, cell-cell junctions and cell adhesion.
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Affiliation(s)
- Lars A T Meijer
- Molecular Cancer Research, Centre for Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
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180
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Pachl F, Ruprecht B, Lemeer S, Kuster B. Characterization of a high field Orbitrap mass spectrometer for proteome analysis. Proteomics 2013; 13:2552-62. [PMID: 23836775 DOI: 10.1002/pmic.201300076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/08/2013] [Accepted: 06/26/2013] [Indexed: 11/06/2022]
Abstract
The field of proteomics continues to be driven by improvements in analytical technology, notably in peptide separation, quantitative MS, and informatics. In this study, we have characterized a hybrid linear ion trap high field Orbitrap mass spectrometer (Orbitrap Elite) for proteomic applications. The very high resolution available on this instrument allows 95% of all peptide masses to be measured with sub-ppm accuracy that in turn improves protein identification by database searching. We further confirm again that mass accuracy in tandem mass spectra is a valuable parameter for improving the success of protein identification. The new CID rapid scan type of the Orbitrap Elite achieves similar performance as higher energy collision induced dissociation fragmentation and both allow the identification of hundreds of proteins from as little as 0.1 ng of protein digest on column. The new instrument outperforms its predecessor the Orbitrap Velos by a considerable margin on each metric assessed that makes it a valuable and versatile tool for MS-based proteomics.
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Affiliation(s)
- Fiona Pachl
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
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181
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Rogers LD, Overall CM. Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics 2013; 12:3532-42. [PMID: 23887885 DOI: 10.1074/mcp.m113.031310] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease. Cleavage generates shorter protein chains displaying neo-N and -C termini, often with new or modified biological activities. Within the past decade, degradomics and terminomics have emerged as significant proteomics subfields dedicated to characterizing proteolysis products as well as natural protein N and C termini. Here we provide an overview of contemporary proteomics-based methods, including specific quantitation, data analysis, and curation considerations, and highlight exciting new and emerging applications within these fields enabling in vivo analysis of proteolytic events.
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Affiliation(s)
- Lindsay D Rogers
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, and Centre for Blood Research, University of British Columbia, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada
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182
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Giansanti P, Stokes MP, Silva JC, Scholten A, Heck AJR. Interrogating cAMP-dependent kinase signaling in Jurkat T cells via a protein kinase A targeted immune-precipitation phosphoproteomics approach. Mol Cell Proteomics 2013; 12:3350-9. [PMID: 23882029 DOI: 10.1074/mcp.o113.028456] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the past decade, mass-spectrometry-based methods have emerged for the quantitative profiling of dynamic changes in protein phosphorylation, allowing the behavior of thousands of phosphorylation sites to be monitored in a single experiment. However, when one is interested in specific signaling pathways, such shotgun methodologies are not ideal because they lack selectivity and are not cost and time efficient with respect to instrument and data analysis time. Here we evaluate and explore a peptide-centric antibody generated to selectively enrich peptides containing the cAMP-dependent protein kinase (PKA) consensus motif. This targeted phosphoproteomic strategy is used to profile temporal quantitative changes of potential PKA substrates in Jurkat T lymphocytes upon prostaglandin E2 (PGE2) stimulation, which increases intracellular cAMP, activating PKA. Our method combines ultra-high-specificity motif-based immunoaffinity purification with cost-efficient stable isotope dimethyl labeling. We identified 655 phosphopeptides, of which 642 (i.e. 98%) contained the consensus motif [R/K][R/K/X]X[pS/pT]. When our data were compared with a large-scale Jurkat T-lymphocyte phosphoproteomics dataset containing more than 10,500 phosphosites, a minimal overlap of 0.2% was observed. This stresses the need for such targeted analyses when the interest is in a particular kinase. Our data provide a resource of likely substrates of PKA, and potentially some substrates of closely related kinases. Network analysis revealed that about half of the observed substrates have been implicated in cAMP-induced signaling. Still, the other half of the here-identified substrates have been less well characterized, representing a valuable resource for future research.
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Affiliation(s)
- Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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183
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SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping. J Proteomics 2013; 91:164-71. [PMID: 23851314 DOI: 10.1016/j.jprot.2013.06.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/25/2013] [Accepted: 06/29/2013] [Indexed: 11/20/2022]
Abstract
UNLABELLED Multidimensional peptide fractionation is widely used in proteomics to reduce the complexity of peptide mixtures prior to mass spectrometric analysis. Here, we describe the sequential use of strong cation exchange and reversed phase liquid chromatography in both basic and acidic pH buffers for separating tryptic peptides from complex mixtures of proteins. Strong cation exchange exclusively separates peptide by their charge state into neutral, singly and multi-charged species. To further reduce complexity, each peptide group was separated by reversed phase liquid chromatography at basic pH and the resultant fractions were analyzed by LC-MS/MS. This workflow was applied to a soluble protein lysate from mouse embryonic fibroblast cells, and more than 5000 proteins from 29,843 peptides were identified. The high selectivity displayed during the SCX step (93% to 100%) and the overlaps between proteins identified from the SCX-separated peptide groups, are interesting assets of the procedure. BIOLOGICAL SIGNIFICANCE The present work shows how complex mixture of peptides can be selectively separated by SCX based essentially on the net charge of peptides. The proposed workflow results in three well-defined subset of peptides of specific amino acid composition, which are representative of the constituent proteins. The very high selectivity obtained (93% to 99%) on the peptide side, underscores for the first time the possibility of SCX chromatography to aid in validating identified peptides.
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184
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Abstract
Motivation: Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra or spectra of non-tryptic digests. Thus, rather than developing a new algorithm for each type of spectra, we develop a universal de novo sequencing algorithm called UniNovo that works well for all types of spectra or even for spectral pairs (e.g. CID/ETD spectral pairs). UniNovo uses an improved scoring function that captures the dependences between different ion types, where such dependencies are learned automatically using a modified offset frequency function. Results: The performance of UniNovo is compared with PepNovo+, PEAKS and pNovo using various types of spectra. The results show that the performance of UniNovo is superior to other tools for ETD spectra and superior or comparable with others for CID and HCD spectra. UniNovo also estimates the probability that each reported reconstruction is correct, using simple statistics that are readily obtained from a small training dataset. We demonstrate that the estimation is accurate for all tested types of spectra (including CID, HCD, ETD, CID/ETD and HCD/ETD spectra of trypsin, LysC or AspN digested peptides). Availability: UniNovo is implemented in JAVA and tested on Windows, Ubuntu and OS X machines. UniNovo is available at http://proteomics.ucsd.edu/Software/UniNovo.html along with the manual. Contact:kwj@ucsd.edu or ppevzner@ucsd.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kyowon Jeong
- Department of Electrical and Computer Engineering and Department of Computer Science and Engineering, University of California-San Diego, CA 92093, USA.
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185
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Kalli A, Smith GT, Sweredoski MJ, Hess S. Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J Proteome Res 2013; 12:3071-86. [PMID: 23642296 DOI: 10.1021/pr3011588] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass-spectrometry-based proteomics has evolved as the preferred method for the analysis of complex proteomes. Undoubtedly, recent advances in mass spectrometry instrumentation have greatly enhanced proteomic analysis. A popular instrument platform in proteomics research is the LTQ-Orbitrap mass analyzer. In this tutorial, we discuss the significance of evaluating and optimizing mass spectrometric settings on the LTQ-Orbitrap during CID data-dependent acquisition (DDA) mode to improve protein and peptide identification rates. We focus on those MS and MS/MS parameters that have been systematically examined and evaluated by several researchers and are commonly used during DDA. More specifically, we discuss the effect of mass resolving power, preview mode for FTMS scan, monoisotopic precursor selection, signal threshold for triggering MS/MS events, number of microscans per MS/MS scan, number of MS/MS events, automatic gain control target value (ion population) for MS and MS/MS, maximum ion injection time for MS/MS, rapid and normal scan rate, and prediction of ion injection time. We furthermore present data from the latest generation LTQ-Orbitrap system, the Orbitrap Elite, along with recommended MS and MS/MS parameters. The Orbitrap Elite outperforms the Orbitrap Classic in terms of scan speed, sensitivity, dynamic range, and resolving power and results in higher identification rates. Several of the optimized MS parameters determined on the LTQ-Orbitrap Classic and XL were easily transferable to the Orbitrap Elite, whereas others needed to be reevaluated. Finally, the Q Exactive and HCD are briefly discussed, as well as sample preparation, LC-optimization, and bioinformatics analysis. We hope this tutorial will serve as guidance for researchers new to the field of proteomics and assist in achieving optimal results.
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Affiliation(s)
- Anastasia Kalli
- Proteome Exploration Laboratory, Division of Biology, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA
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186
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Guthals A, Clauser KR, Frank AM, Bandeira N. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. J Proteome Res 2013; 12:2846-57. [PMID: 23679345 DOI: 10.1021/pr400173d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Full-length de novo sequencing of unknown proteins remains a challenging open problem. Traditional methods that sequence spectra individually are limited by short peptide length, incomplete peptide fragmentation, and ambiguous de novo interpretations. We address these issues by determining consensus sequences for assembled tandem mass (MS/MS) spectra from overlapping peptides (e.g., by using multiple enzymatic digests). We have combined electron-transfer dissociation (ETD) with collision-induced dissociation (CID) and higher-energy collision-induced dissociation (HCD) fragmentation methods to boost interpretation of long, highly charged peptides and take advantage of corroborating b/y/c/z ions in CID/HCD/ETD. Using these strategies, we show that triplet CID/HCD/ETD MS/MS spectra from overlapping peptides yield de novo sequences of average length 70 AA and as long as 200 AA at up to 99% sequencing accuracy.
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Affiliation(s)
- Adrian Guthals
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
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187
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A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics. Nat Biotechnol 2013; 31:557-64. [DOI: 10.1038/nbt.2585] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 04/15/2013] [Indexed: 01/24/2023]
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188
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Loroch S, Dickhut C, Zahedi RP, Sickmann A. Phosphoproteomics--more than meets the eye. Electrophoresis 2013; 34:1483-92. [PMID: 23576030 DOI: 10.1002/elps.201200710] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/22/2013] [Accepted: 03/10/2013] [Indexed: 12/16/2022]
Abstract
PTMs enable cells to adapt to internal and external stimuli in the milliseconds to seconds time regime. Protein phosphorylation is probably the most important of these modifications as it affects protein structure and interactions, critically influencing the life cycle of a cell. In the last 15 years, new insights into phosphorylation have been provided by highly sensitive MS-based approaches combined with specific phosphopeptide enrichment strategies. Although so far research has mainly focused on the discovery and characterization of O-phosphorylation, this review also briefly outlines the current knowledge about N-phosphorylation depicting its ubiquitous relevance. Further, common pitfalls in sample preparation, LC-MS analysis, and subsequent data analysis are discussed as well as issues regarding quality and comparability of studies on protein phosphorylation.
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Affiliation(s)
- Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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189
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Wijten P, van Holten T, Woo LL, Bleijerveld OB, Roest M, Heck AJR, Scholten A. High precision platelet releasate definition by quantitative reversed protein profiling--brief report. Arterioscler Thromb Vasc Biol 2013; 33:1635-8. [PMID: 23640497 DOI: 10.1161/atvbaha.113.301147] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Platelet activation and subsequent protein release play an important role in healthy hemostasis and inflammatory responses, yet the identity and quantity of proteins in the platelet releasate are still debated. Here, we present a reversed releasate proteomics approach to determine unambiguously and quantitatively proteins released from activated platelets. APPROACH AND RESULTS Isolated platelets were mock and fully stimulated after which the released proteins in the supernatant were removed. Using high-end proteomics technology (2D chromatography, stable isotope labeling, electron transfer dissociation, and high collision dissociation fragmentation) allowed us to quantitatively discriminate the released proteins from uncontrolled lysis products. Monitoring the copy numbers of ≈ 4500 platelet proteins, we observed that after stimulation via thrombin and collagen, only 124 (<3%) proteins were significantly released (P<0.05). The released proteins span a concentration range of ≥ 5 orders, as confirmed by ELISA. The released proteins were highly enriched in secretion tags and contained all known factors at high concentrations (>100 ng/mL, eg, thrombospondin, von Willebrand factor, and platelet factor 4). Interestingly, in the lower concentration range of the releasate many novel factors were identified. CONCLUSIONS Our reversed releasate dataset forms the first unambiguous, in depth repository for molecular factors released by platelets.
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Affiliation(s)
- Patrick Wijten
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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190
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Frese CK, Boender AJ, Mohammed S, Heck AJR, Adan RAH, Altelaar AFM. Profiling of diet-induced neuropeptide changes in rat brain by quantitative mass spectrometry. Anal Chem 2013; 85:4594-604. [PMID: 23581470 DOI: 10.1021/ac400232y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neuropeptides are intercellular signal transmitters that play key roles in modulation of many behavioral and physiological processes. Neuropeptide signaling in several nuclei in the hypothalamus contributes to the control of food intake. Additionally, food intake regulation involves neuropeptide signaling in the reward circuitry in the striatum. Here, we analyze neuropeptides extracted from hypothalamus and striatum from rats in four differentially treated dietary groups including a high-fat/high-sucrose diet, mimicking diet-induced obesity. We employ high-resolution tandem mass spectrometry using higher-energy collision dissociation and electron transfer dissociation fragmentation for sensitive identification of more than 1700 unique endogenous peptides, including virtually all key neuropeptides known to be involved in food intake regulation. Label-free quantification of differential neuropeptide expression revealed comparable upregulation of orexigenic and anorexigenic neuropeptides in rats that were fed on a high-fat/high-sucrose diet.
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Affiliation(s)
- Christian K Frese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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191
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Cheng CY, Tsai CF, Chen YJ, Sung TY, Hsu WL. Spectrum-based Method to Generate Good Decoy Libraries for Spectral Library Searching in Peptide Identifications. J Proteome Res 2013; 12:2305-10. [DOI: 10.1021/pr301039b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chia-Ying Cheng
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
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192
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 979] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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193
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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194
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Hennrich ML, Marino F, Groenewold V, Kops GJPL, Mohammed S, Heck AJR. Universal quantitative kinase assay based on diagonal SCX chromatography and stable isotope dimethyl labeling provides high-definition kinase consensus motifs for PKA and human Mps1. J Proteome Res 2013; 12:2214-24. [PMID: 23510141 DOI: 10.1021/pr400074f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In order to understand cellular signaling, a clear understanding of kinase-substrate relationships is essential. Some of these relationships are defined by consensus recognition motifs present in substrates making them amendable for phosphorylation by designated kinases. Here, we explore a method that is based on two sequential steps of strong cation exchange chromatography combined with differential stable isotope labeling, to define kinase consensus motifs with high accuracy. We demonstrate the value of our method by evaluating the motifs of two very distinct kinases: cAMP regulated protein kinase A (PKA) and human monopolar spindle 1 (Mps1) kinase, also known as TTK. PKA is a well-studied basophilic kinase with a relatively well-defined motif and numerous known substrates in vitro and in vivo. Mps1, a kinase involved in chromosome segregation, has been less well characterized. Its substrate specificity is unclear and here we show that Mps1 is an acidophilic kinase with a striking tendency for phosphorylation of threonines. The final outcomes of our work are high-definition kinase consensus motifs for PKA and Mps1. Our generic method, which makes use of proteolytic cell lysates as a source for peptide-substrate libraries, can be implemented for any kinase present in the kinome.
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Affiliation(s)
- Marco L Hennrich
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
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195
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Rolando M, Sanulli S, Rusniok C, Gomez-Valero L, Bertholet C, Sahr T, Margueron R, Buchrieser C. Legionella pneumophila Effector RomA Uniquely Modifies Host Chromatin to Repress Gene Expression and Promote Intracellular Bacterial Replication. Cell Host Microbe 2013; 13:395-405. [DOI: 10.1016/j.chom.2013.03.004] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/06/2013] [Accepted: 03/12/2013] [Indexed: 01/08/2023]
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196
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Jones EA, Schmitz N, Waaijer CJF, Frese CK, van Remoortere A, van Zeijl RJM, Heck AJR, Hogendoorn PCW, Deelder AM, Altelaar AFM, Bovée JVMG, McDonnell LA. Imaging Mass Spectrometry-based Molecular Histology Differentiates Microscopically Identical and Heterogeneous Tumors. J Proteome Res 2013; 12:1847-55. [DOI: 10.1021/pr301190g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Emrys A. Jones
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nicole Schmitz
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Christian K. Frese
- Biomolecular Mass Spectrometry
and Proteomics Group, Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Alexandra van Remoortere
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - René J. M. van Zeijl
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry
and Proteomics Group, Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - André M. Deelder
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular Mass Spectrometry
and Proteomics Group, Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Liam A. McDonnell
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
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197
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Breitwieser FP, Colinge J. Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins. J Proteomics 2013; 90:77-84. [PMID: 23470796 PMCID: PMC3759844 DOI: 10.1016/j.jprot.2013.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/21/2013] [Accepted: 02/21/2013] [Indexed: 12/26/2022]
Abstract
The establishment of extremely powerful proteomics platforms able to map thousands of modification sites, e.g. phosphorylations or acetylations, over entire proteomes calls for equally powerful software tools to effectively extract useful and reliable information from such complex datasets. We present a new quantitative PTM analysis platform aimed at processing iTRAQ or Tandem Mass Tags (TMT) labeled peptides. It covers a broad range of needs associated with proper PTM ratio analysis such as PTM localization validation, robust ratio computation and statistical assessment, and navigable user report generation. IsobarPTM is made available as an R Bioconductor package and it can be run from the command line by non R specialists. Biological significance “IsobarPTM is a new software tool facilitating the quantitative analysis of protein modification regulation streamlining important issues related to PTM localization and statistical modeling. Users are provided with a navigable spreadsheet report, which also annotate already public modification sites.” This article is part of a Special Issue entitled: From Genome to Proteome: Open Innovations. IsobarPTM is a new open source software tool to analyze PTM regulation. Quantitative iTRAQ and TMT data are supported. Whole set of functionalities from PTM size localization to statistical modeling Navigable user reports are generated automatically. Available as R Bioconductor package
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Affiliation(s)
| | - Jacques Colinge
- Corresponding author. Tel.: + 43 14016070020; fax: + 43 140160970000.
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198
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Abstract
Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary, and quaternary structures as well as the dynamics that accompany functional cycles and catalysis.
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Affiliation(s)
- Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The NPI-Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, California 90095, United States.
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199
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Creese AJ, Shimwell NJ, Larkins KPB, Heath JK, Cooper HJ. Probing the complementarity of FAIMS and strong cation exchange chromatography in shotgun proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:431-43. [PMID: 23400772 PMCID: PMC3586169 DOI: 10.1007/s13361-012-0544-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/08/2012] [Accepted: 11/11/2012] [Indexed: 05/25/2023]
Abstract
High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) offers benefits for the analysis of complex proteomics samples. Advantages include increased dynamic range, increased signal-to-noise, and reduced interference from ions of similar m/z. FAIMS also separates isomers and positional variants. An alternative, and more established, method of reducing sample complexity is prefractionation by use of strong cation exchange chromatography. Here, we have compared SCX-LC-MS/MS with LC-FAIMS-MS/MS for the identification of peptides and proteins from whole cell lysates from the breast carcinoma SUM52 cell line. Two FAIMS approaches are considered: (1) multiple compensation voltages within a single LC-MS/MS analysis (internal stepping) and (2) repeat LC-MS/MS analyses at different and fixed compensation voltages (external stepping). We also consider the consequence of the fragmentation method (electron transfer dissociation or collision-induced dissociation) on the workflow performance. The external stepping approach resulted in a greater number of protein and peptide identifications than the internal stepping approach for both ETD and CID MS/MS, suggesting that this should be the method of choice for FAIMS proteomics experiments. The overlap in protein identifications from the SCX method and the external FAIMS method was ~25% for both ETD and CID, and for peptides was less than 20%. The lack of overlap between FAIMS and SCX highlights the complementarity of the two techniques. Charge state analysis of the peptide assignments showed that the FAIMS approach identified a much greater proportion of triply-charged ions.
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Affiliation(s)
- Andrew J. Creese
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Neil J. Shimwell
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
- Present Address: School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Katherine P. B. Larkins
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - John K. Heath
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Helen J. Cooper
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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200
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Rudashevskaya EL, Breitwieser FP, Huber ML, Colinge J, Müller AC, Bennett KL. Multiple and Sequential Data Acquisition Method: An Improved Method for Fragmentation and Detection of Cross-Linked Peptides on a Hybrid Linear Trap Quadrupole Orbitrap Velos Mass Spectrometer. Anal Chem 2013; 85:1454-61. [DOI: 10.1021/ac302251f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Elena L. Rudashevskaya
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian P. Breitwieser
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marie L. Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department
of Dermatology, Division
of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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