1
|
Gosset-Erard C, Aubriet F, Leize-Wagner E, François YN, Chaimbault P. Hyphenation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with separation methods: The art of compromises and the possible - A review. Talanta 2023; 257:124324. [PMID: 36780779 DOI: 10.1016/j.talanta.2023.124324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
This review provides an overview of the online hyphenation of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with separation methods to date. The online coupling between separation techniques (gas and liquid chromatography, capillary electrophoresis) and FT-ICR MS essentially raises questions of compromise and is not look as straightforward as hyphenation with other analyzers (QTOF-MS for instance). FT-ICR MS requires time to reach its highest resolving power and accuracy in mass measurement capabilities whereas chromatographic and electrophoretic peaks are transient. In many applications, the strengths and the weaknesses of each technique are balanced by their hyphenation. Untargeted "Omics" (e.g. proteomics, metabolomics, petroleomics, …) is one of the main areas of application for FT-ICR MS hyphenated to online separation techniques because of the complexity of the sample. FT-ICR MS achieves the required high mass measurement accuracy to determine accurate molecular formulae and resolution for isobar distinction. Meanwhile separation techniques highlight isomers and reduce the ion suppression effects extending the dynamic range. Even if the implementation of FT-ICR MS hyphenated with online separation methods is a little trickier (the art of compromise), this review shows that it provides unparalleled results to the scientific community (the art of the possible), along with raising the issue of its future in the field with the relentless technological progress.
Collapse
Affiliation(s)
- Clarisse Gosset-Erard
- Université de Lorraine, LCP-A2MC, F-57000, Metz, France; Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | | |
Collapse
|
2
|
Aydoğan C, Beltekin B, Alharthi S, Ağca CA, Erdoğan İY. Nano-liquid chromatography with monolithic stationary phase based on naphthyl monomer for proteomics analysis. J Chromatogr A 2023; 1690:463804. [PMID: 36689803 DOI: 10.1016/j.chroma.2023.463804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Monolithic poly(2-vinylnaphthalene-co-divinylbenzene) columns were introduced, for the first time, and were evaluated as the separation media for nano-liquid chromatography (nano-LC). These columns were prepared by in-situ polymerization of 2-vinylnaphthalene (2-VNA) as the functional monomer and divinylbenzene (DVB) as the crosslinker in a fused silica capillary column of 50 µm i.d. Various porogenic solvents, including tetrahydrofuran (THF), dodecanol and toluene were used for morphology optimization. Final monolithic column (referred to as VNA column) was characterized by using scanning electron microscopy (SEM) and chromatographic analyses. Alkylbenzenes (ABs), and polyaromatic hydrocarbons (PAHs) were separated using the VNA column while the column offered excellent hydrophobic and π-π interactions under reversed-phase conditions. Theoretical plates number up to 41,200 plates/m in isocratic mode for ethylbenzene could be achieved. The potential of the final VNA column was demonstrated with a gradient elution in the separation of six intact proteins, including ribonuclease A (RNase A), cytochrome C (Cyt C), lysozyme (Lys), β-lactoglobulin (β-lac), myoglobin (My) and α-chymotrypsinogen (α-chym) in nano LC system. The column was then applied to the peptide analysis of trypsin digested cytochrome C, allowing a high peak capacity up to 1440 and the further proteomics analysis of COS-7 cell line was attempted applying the final monolithic column in nano-LC UV system.
Collapse
Affiliation(s)
- Cemil Aydoğan
- Food Analysis and Research Laboratory, Bingöl University, Bingöl, Türkiye; Department of Food Engineering, Bingöl University, Bingöl, Türkiye; Department of Chemistry, Bingöl University, Bingöl, Türkiye.
| | - Büşra Beltekin
- Food Analysis and Research Laboratory, Bingöl University, Bingöl, Türkiye
| | - Sarah Alharthi
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif, 21944 Saudi Arabia
| | - Can Ali Ağca
- Department of Molecular Biology, Bingöl University, Bingöl, Türkiye
| | - İbrahim Y Erdoğan
- Department of Chemistry, Bingöl University, Bingöl, Türkiye; Faculty of Health Sciences, Bingöl University, Bingöl, Türkiye
| |
Collapse
|
3
|
Winkels K, Koudelka T, Tholey A. Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags. J Proteome Res 2021; 20:4495-4506. [PMID: 34338531 DOI: 10.1021/acs.jproteome.1c00460] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While identification-centric (qualitative) top-down proteomics (TDP) has seen rapid progress in the recent past, the quantification of intact proteoforms within complex proteomes is still challenging. The by far mostly applied approach is label-free quantification, which, however, provides limited multiplexing capacity, and its use in combination with multidimensional separation is encountered with a number of problems. Isobaric labeling, which is a standard quantification approach in bottom-up proteomics, circumvents these limitations. Here, we introduce the application of thiol-directed isobaric labeling for quantitative TDP. For this purpose, we analyzed the labeling efficiency and optimized tandem mass spectrometry parameters for optimal backbone fragmentation for identification and reporter ion formation for quantification. Two different separation schemes, gel-eluted liquid fraction entrapment electrophoresis × liquid chromatography-mass spectrometry (LC-MS) and high/low-pH LC-MS, were employed for the analyses of either Escherichia coli (E. coli) proteomes or combined E. coli/yeast samples (two-proteome interference model) to study potential ratio compression. While the thiol-directed labeling introduces a bias in the quantifiable proteoforms, being restricted to Cys-containing proteoforms, our approach showed excellent accuracy in quantification, which is similar to that achievable in bottom-up proteomics. For example, 876 proteoforms could be quantified with high accuracy in an E. coli lysate. The LC-MS data were deposited to the ProteomeXchange with the dataset identifier PXD026310.
Collapse
Affiliation(s)
- Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel 24105, Germany
| | - Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel 24105, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel 24105, Germany
| |
Collapse
|
4
|
Yu D, Wang Z, Cupp-Sutton KA, Guo Y, Kou Q, Smith K, Liu X, Wu S. Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1336-1344. [PMID: 33725447 PMCID: PMC8323476 DOI: 10.1021/jasms.0c00464] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Labeling approaches using isobaric chemical tags (e.g., isobaric tagging for relative and absolute quantification, iTRAQ and tandem mass tag, TMT) have been widely applied for the quantification of peptides and proteins in bottom-up MS. However, until recently, successful applications of these approaches to top-down proteomics have been limited because proteins tend to precipitate and "crash" out of solution during TMT labeling of complex samples making the quantification of such samples difficult. In this study, we report a top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples. To reduce the sample complexity and remove large proteins from complex samples, we developed a filter-SEC technique that combines a molecular weight cutoff filtration step with high-performance size exclusion chromatography (SEC) separation. No protein precipitation was observed in filtered samples under the intact protein-level TMT labeling conditions. The proposed top-down TMT MS platform enables high-throughput analysis of intact proteoforms, allowing for the identification and quantification of hundreds of intact proteoforms from Escherichia coli cell lysates. To our knowledge, this represents the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
Collapse
Affiliation(s)
- Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Qiang Kou
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Xiaowen Liu
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| |
Collapse
|
5
|
Zhou M, Malhan N, Ahkami AH, Engbrecht K, Myers G, Dahlberg J, Hollingsworth J, Sievert JA, Hutmacher R, Madera M, Lemaux PG, Hixson KK, Jansson C, Paša-Tolić L. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. Methods 2020; 184:29-39. [DOI: 10.1016/j.ymeth.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
|
6
|
Aydoğan C, Rigano F, Krčmová LK, Chung DS, Macka M, Mondello L. Miniaturized LC in Molecular Omics. Anal Chem 2020; 92:11485-11497. [DOI: 10.1021/acs.analchem.0c01436] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Cemil Aydoğan
- Biochemistry Division, Department of Chemistry, Bingöl University, Bingöl 12000,Turkey
- Department of Food Engineering, Bingöl University, Bingöl 12000,Turkey
| | - Francesca Rigano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
| | - Lenka Kujovská Krčmová
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, Hradec Králové 500 05, Czech Republic
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Sokolská 581, Hradec Králové 500 05, Czech Republic
| | - Doo Soo Chung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Mirek Macka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00Brno, Czech Republic
- School of Natural Sciences and Australian Centre for Research on Separation Science (ACROSS), University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
- Department of Sciences and Technologies for Human and Environment, University Campus Bio-Medico of Rome, Rome I-00128, Italy
- BeSep s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
| |
Collapse
|
7
|
Abstract
Top-down mass spectrometry (MS) analyzes intact proteins at the proteoform level, which allows researchers to better understand the functions of protein modifications. Recently, top-down proteomics has increased in popularity due to advancements in high-resolution mass spectrometers, increased efficiency in liquid chromatography (LC) separation, and advances in data analysis software. Some unique protein proteoforms, which have been distinguished using top-down MS, have even been shown to exhibit marked variation in biological function compared to similar proteoforms. However, the qualitative identification of a particular proteoform may not be enough to determine the biological relevance of that proteoform. Quantitative top-down MS methods have been notably applied to the study of the differing biological functions of protein proteoforms and have allowed researchers to explore proteomes at the proteoform, rather than the peptide, level. Here, we review the top-down MS methods that have been used to quantitatively identify intact proteins, discuss current applications of quantitative top-down MS analysis, and present new areas where quantitative top-down MS analysis may be implemented.
Collapse
Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK 73019-5251, USA.
| | | |
Collapse
|
8
|
Liu Z, Wang R, Liu J, Sun R, Wang F. Global Quantification of Intact Proteins via Chemical Isotope Labeling and Mass Spectrometry. J Proteome Res 2019; 18:2185-2194. [PMID: 30990045 DOI: 10.1021/acs.jproteome.9b00071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although thousands of intact proteins have been feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99.2% for complex intact protein samples extracted from HeLa cells. Further, the pTop 2.0 software is developed for automated quantification of intact proteoforms in a high-throughput manner. The high quantification accuracy and reproducibility of this strategy have been demonstrated for both standard and complex cellular protein samples. A total of 2283 intact proteoforms originated from 660 protein accessions are successfully quantified under anaerobic and aerobic conditions and the differentially expressed proteins are observed to be involved in the important biological processes such as stress response.
Collapse
Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , 116023 , China
| | - Ruimin Wang
- Institute of Computing Technology , Chinese Academy of Sciences , Beijing , 100190 , China
| | - Jing Liu
- College of Pharmacy , Dalian Medical University , Dalian , 116044 , China
| | - Ruixiang Sun
- Institute of Computing Technology , Chinese Academy of Sciences , Beijing , 100190 , China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , 116023 , China
| |
Collapse
|
9
|
Lin Z, Wei L, Cai W, Zhu Y, Tucholski T, Mitchell SD, Guo W, Ford SP, Diffee GM, Ge Y. Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome. Mol Cell Proteomics 2019; 18:594-605. [PMID: 30591534 PMCID: PMC6398208 DOI: 10.1074/mcp.tir118.001086] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Determining changes in protein expression and post-translational modifications (PTMs) is crucial for elucidating cellular signal transduction and disease mechanisms. Conventional antibody-based approaches have inherent problems such as the limited availability of high-quality antibodies and batch-to-batch variation. Top-down mass spectrometry (MS)-based proteomics has emerged as the most powerful method for characterization and quantification of protein modifications. Nevertheless, robust methods to simultaneously determine changes in protein expression and PTMs remain lacking. Herein, we have developed a straightforward and robust top-down liquid chromatography (LC)/MS-based targeted proteomics platform for simultaneous quantification of protein expression and PTMs with high throughput and high reproducibility. We employed this method to analyze the sarcomeric subproteome from various muscle types of different species, which successfully revealed skeletal muscle heterogeneity and cardiac developmental changes in sarcomeric protein isoform expression and PTMs. As demonstrated, this targeted top-down proteomics platform offers an excellent 'antibody-independent' alternative for the accurate quantification of sarcomeric protein expression and PTMs concurrently in complex mixtures, which is generally applicable to different species and various tissue types.
Collapse
Affiliation(s)
- Ziqing Lin
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Liming Wei
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ¶Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Yanlong Zhu
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Trisha Tucholski
- **Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Stanford D Mitchell
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Wei Guo
- ‡‡Department of Animal Science, Fetal Programming Center, University of Wyoming, Laramie, Wyoming 82071
| | - Stephen P Ford
- ‡‡Department of Animal Science, Fetal Programming Center, University of Wyoming, Laramie, Wyoming 82071
| | - Gary M Diffee
- §§Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53705
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705;
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
- **Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| |
Collapse
|
10
|
Chang HY, Chen CT, Ko CL, Chen YJ, Chen YJ, Hsu WL, Juo CG, Sung TY. iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Anal Chem 2017; 89:13128-13136. [DOI: 10.1021/acs.analchem.7b02343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hui-Yin Chang
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Tai Chen
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chu-Ling Ko
- Department
of Computer Science, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chiun-Gung Juo
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- PharmaEssentia Corp., Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
11
|
Lv Y. Proteome-wide profiling of protein lysine acetylation in Aspergillus flavus. PLoS One 2017; 12:e0178603. [PMID: 28582408 PMCID: PMC5459447 DOI: 10.1371/journal.pone.0178603] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 05/16/2017] [Indexed: 01/18/2023] Open
Abstract
Protein lysine acetylation is a prevalent post-translational modification that plays pivotal roles in various biological processes in both prokaryotes and eukaryotes. Aspergillus flavus, as an aflatoxin-producing fungus, has attracted tremendous attention due to its health impact on agricultural commodities. Here, we performed the first lysine-acetylome mapping in this filamentous fungus using immune-affinity-based purification integrated with high-resolution mass spectrometry. Overall, we identified 1383 lysine-acetylation sites in 652 acetylated proteins, which account for 5.18% of the total proteins in A. flavus. According to bioinformatics analysis, the acetylated proteins are involved in various cellular processes involving the ribosome, carbon metabolism, antibiotic biosynthesis, secondary metabolites, and the citrate cycle and are distributed in diverse subcellular locations. Additionally, we demonstrated for the first time the acetylation of fatty acid synthase α and β encoded by aflA and aflB involved in the aflatoxin-biosynthesis pathway (cluster 54), as well as backbone enzymes from secondary metabolite clusters 20 and 21 encoded by AFLA_062860 and AFLA_064240, suggesting important roles for acetylation associated with these processes. Our findings illustrating abundant lysine acetylation in A. flavus expand our understanding of the fungal acetylome and provided insight into the regulatory roles of acetylation in secondary metabolism.
Collapse
Affiliation(s)
- Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
- * E-mail:
| |
Collapse
|
12
|
A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis. Proteomes 2017; 5:proteomes5020011. [PMID: 28387712 PMCID: PMC5489772 DOI: 10.3390/proteomes5020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.
Collapse
|
13
|
Quijada JV, Schmitt ND, Salisbury JP, Auclair JR, Agar JN. Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism. Anal Chem 2016; 88:11139-11146. [PMID: 27744677 DOI: 10.1021/acs.analchem.6b03234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable isotope labeling techniques for quantitative top-down proteomics face unique challenges. These include unpredictable mass shifts following isotope labeling, which impedes analysis of unknown proteins and complex mixtures and exponentially greater susceptibility to incomplete isotope incorporation, manifesting as broadening of labeled intact protein peaks. Like popular bottom-up isotope labeling techniques, most top-down labeling methods are restricted to defined media/feed as well as amino acid auxotrophic organisms. We present a labeling method optimized for top-down proteomics that overcomes these challenges. We demonstrated this method through the spiking of 13C-sugar or 2H-water into standard laboratory feedstocks, resulting in tunable intact protein mass increases (TIPMI). After mixing of labeled and unlabeled samples, direct comparison of light and heavy peaks allowed for the relative quantitation of intact proteins in three popular model organisms, including prokaryotic and eukaryotic microorganisms and an animal. This internal standard method proved to be more accurate than label-free quantitation in our hands. Advantages over top-down SILAC include working equally well in nutrient-rich media, conceivably expanding applicability to any organism and all classes of biomolecules, not requiring high-resolving power MS for quantitation and being relatively inexpensive.
Collapse
Affiliation(s)
- Jeniffer V Quijada
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Nicholas D Schmitt
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Joseph P Salisbury
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jared R Auclair
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Department of Pharmaceutical Sciences, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| |
Collapse
|
14
|
Fang H, Xiao K, Li Y, Yu F, Liu Y, Xue B, Tian Z. Intact Protein Quantitation Using Pseudoisobaric Dimethyl Labeling. Anal Chem 2016; 88:7198-205. [PMID: 27359340 DOI: 10.1021/acs.analchem.6b01388] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein structural and functional studies rely on complete qualitative and quantitative information on protein species (proteoforms); thus, it is important to quantify differentially expressed proteins at their molecular level. Here we report our development of universal pseudoisobaric dimethyl labeling (pIDL) of amino groups at both the N-terminal and lysine residues for relative quantitation of intact proteins. Initial proof-of-principle study was conducted on standard protein myoglobin and hepatocellular proteomes (HepG2 vs LO2). The amino groups from both the N-terminal and lysine were dimethylated with HXHO (X = (13)C or C) and NaBY3CN (Y = H or D). At the standard protein level, labeling efficiency, effect of product ion size, and mass resolution on quantitation accuracy were explored; and a good linear quantitation dynamic range up to 50-fold was obtained. For the hepatocellular proteome samples, 33 proteins were quantified with RSD ≤ 10% from one-dimensional reversed phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) analysis of the 1:1 mixed samples. The method in this study can be extended to quantitation of other intact proteome systems. The universal "one-pot" dimethyl labeling of all the amino groups in a protein without the need of preblocking of those on the lysine residues is made possible by protein identification and quantitation analysis using ProteinGoggle 2.0 with customized databases of both precursor and product ions containing heavy isotopes.
Collapse
Affiliation(s)
- Houqin Fang
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Kaijie Xiao
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Yunhui Li
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Fan Yu
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Yan Liu
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Bingbing Xue
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| |
Collapse
|
15
|
Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down Proteomics and the Analysis of Proteoforms. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:499-519. [PMID: 27306313 PMCID: PMC5373801 DOI: 10.1146/annurev-anchem-071015-041550] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.
Collapse
Affiliation(s)
- Timothy K Toby
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
| | - Luca Fornelli
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| |
Collapse
|
16
|
Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature. Sci Rep 2015; 5:14582. [PMID: 26416011 PMCID: PMC4586720 DOI: 10.1038/srep14582] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/04/2015] [Indexed: 01/01/2023] Open
Abstract
To investigate the changes in transcript and relative protein levels in response to temperature, complementary transcriptomic and proteomic analyses were used to identify changes in Aspergillus flavus grown at 28 °C and 37 °C. A total of 3,886 proteins were identified, and 2,832 proteins were reliably quantified. A subset of 664 proteins was differentially expressed upon temperature changes and enriched in several Kyoto Encyclopedia of Genes and Genomes pathways: translation-related pathways, metabolic pathways, and biosynthesis of secondary metabolites. The changes in protein profiles showed low congruency with alterations in corresponding transcript levels, indicating that post-transcriptional processes play a critical role in regulating the protein level in A. flavus. The expression pattern of proteins and transcripts related to aflatoxin biosynthesis showed that most genes were up-regulated at both the protein and transcript level at 28 °C. Our data provide comprehensive quantitative proteome data of A. flavus at conducive and nonconducive temperatures.
Collapse
|
17
|
Klitgaard A, Nielsen JB, Frandsen RJN, Andersen MR, Nielsen KF. Combining Stable Isotope Labeling and Molecular Networking for Biosynthetic Pathway Characterization. Anal Chem 2015; 87:6520-6. [PMID: 26020678 DOI: 10.1021/acs.analchem.5b01934] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Filamentous fungi are a rich source of bioactive compounds, ranging from statins over immunosuppressants to antibiotics. The coupling of genes to metabolites is of large commercial interest for production of the bioactives of the future. To this end, we have investigated the use of stable isotope labeled amino acids (SILAAs). SILAAs were added to the cultivation media of the filamentous fungus Aspergillus nidulans for the study of the cyclic tetrapeptide nidulanin A. Analysis by UHPLC-TOFMS confirmed that the SILAAs were incorporated into produced nidulanin A, and the change in observed m/z could be used to determine whether a compound (known or unknown) incorporated any of the added amino acids. Samples were then analyzed using MS/MS and the data used to perform molecular networking. The molecular network revealed several known and unknown compounds that were also labeled. Assisted by the isotope labeling, it was possible to determine the sequence of several of the compounds, one of which was the known metabolite fungisporin, not previously described in A. nidulans. Several novel analogues of nidulanin A and fungisporin were detected and tentatively identified, and it was determined that these metabolites were all produced by the same nonribosomal peptide synthase. The combination of stable isotope labeling and molecular network generation was shown to very effective for the automated detection of structurally related nonribosomal peptides, while the labeling was effective for determination of the peptide sequence, which could be used to provide information on biosynthesis of bioactive compounds.
Collapse
Affiliation(s)
- Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jakob B Nielsen
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Rasmus J N Frandsen
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| |
Collapse
|
18
|
Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
19
|
Gregorich ZR, Ge Y. Top-down proteomics in health and disease: challenges and opportunities. Proteomics 2014; 14:1195-210. [PMID: 24723472 DOI: 10.1002/pmic.201300432] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/10/2014] [Accepted: 03/24/2014] [Indexed: 01/06/2023]
Abstract
Proteomics is essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in human disease; however, the unique characteristics of the human proteome, which include a high dynamic range of protein expression and extreme complexity due to a plethora of PTMs and sequence variations, make such analyses challenging. An emerging "top-down" MS-based proteomics approach, which provides a "bird's eye" view of all proteoforms, has unique advantages for the assessment of PTMs and sequence variations. Recently, a number of studies have showcased the potential of top-down proteomics for the unraveling of disease mechanisms and discovery of new biomarkers. Nevertheless, the top-down approach still faces significant challenges in terms of protein solubility, separation, and the detection of large intact proteins, as well as underdeveloped data analysis tools. Consequently, new technological developments are urgently needed to advance the field of top-down proteomics. Herein, we intend to provide an overview of the recent applications of top-down proteomics in biomedical research. Moreover, we will outline the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases.
Collapse
Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | |
Collapse
|
20
|
Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014; 14:547-65. [PMID: 24376008 DOI: 10.1002/pmic.201300403] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
Collapse
Affiliation(s)
- Andreas Otto
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Germany
| | | | | |
Collapse
|
21
|
Comparative analysis of secretomes in basidiomycete fungi. J Proteomics 2014; 102:28-43. [DOI: 10.1016/j.jprot.2014.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/19/2014] [Accepted: 03/03/2014] [Indexed: 12/29/2022]
|
22
|
Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA, Coon JJ. Neutron-encoded mass signatures for quantitative top-down proteomics. Anal Chem 2014; 86:2314-9. [PMID: 24475910 PMCID: PMC3983007 DOI: 10.1021/ac403579s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ability to acquire highly accurate quantitative data is an increasingly important part of any proteomics experiment, whether shotgun or top-down approaches are used. We recently developed a quantitation strategy for peptides based on neutron encoding, or NeuCode SILAC, which uses closely spaced heavy isotope-labeled amino acids and high-resolution mass spectrometry to provide quantitative data. We reasoned that the strategy would also be applicable to intact proteins and could enable robust, multiplexed quantitation for top-down experiments. We used yeast lysate labeled with either (13)C6(15)N2-lysine or (2)H8-lysine, isotopologues of lysine that are spaced 36 mDa apart. Proteins having such close spacing cannot be distinguished during a medium resolution scan, but upon acquiring a high-resolution scan, the two forms of the protein with each amino acid are resolved and the quantitative information revealed. An additional benefit NeuCode SILAC provides for top down is that the spacing of the isotope peaks indicates the number of lysines present in the protein, information that aids in identification. We used NeuCode SILAC to quantify several hundred isotope distributions, manually identify and quantify proteins from 1:1, 3:1, and 5:1 mixed ratios, and demonstrate MS(2)-based quantitation using ETD.
Collapse
Affiliation(s)
- Timothy W Rhoads
- Department of Chemistry, ‡Department of Biomolecular Chemistry, §Genome Center, and ∇Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Liuni P, Wilson DJ. Understanding and optimizing electrospray ionization techniques for proteomic analysis. Expert Rev Proteomics 2014; 8:197-209. [DOI: 10.1586/epr.10.111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
24
|
Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. High-throughput proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:427-454. [PMID: 25014346 DOI: 10.1146/annurev-anchem-071213-020216] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
Collapse
|
25
|
Ding W, Qiu P, Liu YH, Feng W. Current Omics Technologies in Biomarker Discovery. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Biomarkers are playing an increasingly important role in drug discovery and development and can be applied for many purposes, including disease mechanism study, diagnosis, prognosis, staging, and treatment selection. Advances in high-throughput “omics” technologies, including genomics, transcriptomics, proteomics and metabolomics, significantly accelerate the pace of biomarker discovery. Comprehensive molecular profiling using these “omics” technology has become a field of intensive research aiming at identifying biomarkers relevant for improved diagnostics and therapeutics. Although each “omics” technology plays important roles in biomarker research, different “omics” platforms have different strengths and limitations. This chapter aims to give an overview of these “omics” technologies and their current application in the biomarker discovery.
Collapse
|
26
|
Russell JD, Scalf M, Book AJ, Ladror DT, Vierstra RD, Smith LM, Coon JJ. Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry. PLoS One 2013; 8:e58157. [PMID: 23536786 PMCID: PMC3594244 DOI: 10.1371/journal.pone.0058157] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 02/03/2013] [Indexed: 11/18/2022] Open
Abstract
Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.
Collapse
Affiliation(s)
- Jason D. Russell
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Adam J. Book
- Department of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Daniel T. Ladror
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Richard D. Vierstra
- Department of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
27
|
Catherman AD, Li M, Tran JC, Durbin KR, Compton PD, Early BP, Thomas PM, Kelleher NL. Top down proteomics of human membrane proteins from enriched mitochondrial fractions. Anal Chem 2013; 85:1880-8. [PMID: 23305238 DOI: 10.1021/ac3031527] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The interrogation of intact integral membrane proteins has long been a challenge for biological mass spectrometry. Here, we demonstrate the application of top down mass spectrometry to whole membrane proteins below 60 kDa with up to 8 transmembrane helices. Analysis of enriched mitochondrial membrane preparations from human cells yielded identification of 83 integral membrane proteins, along with 163 membrane-associated or soluble proteins, with a median q value of 3 × 10(-10). An analysis of matching fragment ions demonstrated that significantly more fragment ions were found within transmembrane domains than would be expected based upon the observed protein sequence. In total, 46 proteins from the complexes of oxidative phosphorylation were identified which exemplifies the increasing ability of top down proteomics to provide extensive coverage in a biological network.
Collapse
Affiliation(s)
- Adam D Catherman
- Department of Chemistry, the Chemistry of Life Processes Institute, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, 60208, United States
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Cappadona S, Baker PR, Cutillas PR, Heck AJR, van Breukelen B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012. [PMID: 22821268 DOI: 10.1007/s00726-012-1289-1288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.
Collapse
Affiliation(s)
- Salvatore Cappadona
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | | | | | | | | |
Collapse
|
29
|
Cappadona S, Baker PR, Cutillas PR, Heck AJR, van Breukelen B. Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012; 43:1087-108. [PMID: 22821268 PMCID: PMC3418498 DOI: 10.1007/s00726-012-1289-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 04/03/2012] [Indexed: 10/31/2022]
Abstract
Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.
Collapse
Affiliation(s)
- Salvatore Cappadona
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre 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
| | - Peter R. Baker
- Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, University of California San Francisco, San Francisco, USA
| | - Pedro R. Cutillas
- Analytical Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre 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
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre 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
- Netherlands Bioinformatics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
30
|
Adou K, Johnston MV, Dykins JL. Targeted Absolute Quantification of Intact Proteins by Reversed Phase Liquid Chromatography-Mass Spectrometry, Charge Reduced Electrospray, and Condensation Particle Counting. Anal Chem 2012; 84:6981-5. [DOI: 10.1021/ac300950w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kouame Adou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
| | - Murray V. Johnston
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
| | - John L. Dykins
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
| |
Collapse
|
31
|
Collier TS, Muddiman DC. Analytical strategies for the global quantification of intact proteins. Amino Acids 2012; 43:1109-17. [PMID: 22821264 DOI: 10.1007/s00726-012-1285-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
The quantification of intact proteins is a relatively recent development in proteomics. In eukaryotic organisms, proteins are present as multiple isoforms as the result of variations in genetic code, alternative splicing, post-translational modification and other processing events. Understanding the identities and biological functions of these isoforms and how their concentrations vary across different states is the central goal of proteomics. To date, the bulk of proteomics research utilizes a "bottom-up" approach, digesting proteins into their more manageable constitutive peptides, but sacrificing information about the specific isoform and combinations of post-translational modifications present on the protein. Very specific strategies for protein quantification such as the enzyme-linked immunosorbent assay and Western blot are commonplace in laboratories and clinics, but impractical for the study of global biological changes. Herein, we describe strategies for the quantification of intact proteins, their distinct advantages, and challenges to their employment. Techniques contained in this review include the more traditional and widely employed methodology of differential gel electrophoresis and more recently developed mass spectrometry-based techniques including metabolic labeling, chemical labeling, and label-free methodologies.
Collapse
Affiliation(s)
- Timothy S Collier
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | |
Collapse
|
32
|
Kellie JF, Catherman AD, Durbin KR, Tran JC, Tipton JD, Norris JL, Witkowski CE, Thomas PM, Kelleher NL. Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry. Anal Chem 2011; 84:209-15. [PMID: 22103811 DOI: 10.1021/ac202384v] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As the process of top-down mass spectrometry continues to mature, we benchmark the next installment of an improving methodology that incorporates a tube-gel electrophoresis (TGE) device to separate intact proteins by molecular mass. Top-down proteomics is accomplished in a robust fashion to yield the identification of hundreds of unique proteins, many of which correspond to multiple protein forms. The TGE platform separates 0-50 kDa proteins extracted from the yeast proteome into 12 fractions prior to automated nanocapillary LC-MS/MS in technical triplicate. The process may be completed in less than 72 h. From this study, 530 unique proteins and 1103 distinct protein species were identified and characterized, thus representing the highest coverage to date of the Saccharomyces cerevisiae proteome using top-down proteomics. The work signifies a significant step in the maturation of proteomics based on direct measurement and fragmentation of intact proteins.
Collapse
Affiliation(s)
- John F Kellie
- Department of Chemistry, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University, 2145 North Sheridan Road, Evanston, Illinois 60208, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Hung CW, Tholey A. Tandem Mass Tag Protein Labeling for Top-Down Identification and Quantification. Anal Chem 2011; 84:161-70. [DOI: 10.1021/ac202243r] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chien-Wen Hung
- Institut für Experimentelle Medizin—AG Systematische Proteomforschung, Christian-Albrechts-Universität, Niemannsweg 11, 24105 Kiel, Germany
| | - Andreas Tholey
- Institut für Experimentelle Medizin—AG Systematische Proteomforschung, Christian-Albrechts-Universität, Niemannsweg 11, 24105 Kiel, Germany
| |
Collapse
|
34
|
Zhou H, Ning Z, E. Starr A, Abu-Farha M, Figeys D. Advancements in Top-Down Proteomics. Anal Chem 2011; 84:720-34. [DOI: 10.1021/ac202882y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Zhibing Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| |
Collapse
|
35
|
Hoopmann MR, Chavez JD, Bruce JE. SILACtor: software to enable dynamic SILAC studies. Anal Chem 2011; 83:8403-10. [PMID: 21954881 DOI: 10.1021/ac2017053] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a versatile tool in proteomics that has been used to explore protein turnover on a large scale. However, these studies pose a significant undertaking that can be greatly simplified through the use of computational tools that automate the data analysis. While SILAC technology has enjoyed rapid adoption through the availability of several software tools, algorithms do not exist for the automated analysis of protein turnover data generated using SILAC technology. Presented here is a software tool, SILACtor, designed to trace and compare SILAC-labeled peptides across multiple time points. SILACtor is used to profile protein turnover rates for more than 500 HeLa cell proteins using a SILAC label-chase approach. Additionally, SILACtor contains a method for the automated generation of accurate mass and retention time inclusion lists that target peptides of interest showing fast or slow turnover rates relative to the other peptides observed in the samples. SILACtor enables improved protein turnover studies using SILAC technology and also provides a framework for features extensible to comparative SILAC analyses and targeted methods.
Collapse
Affiliation(s)
- Michael R Hoopmann
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109-4717, United States
| | | | | |
Collapse
|
36
|
Collier TS, Randall SM, Sarkar P, Rao BM, Dean RA, Muddiman DC. Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2524-2532. [PMID: 21818813 DOI: 10.1002/rcm.5151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Protein quantification is one of the principal goals of mass spectrometry (MS)-based proteomics, and many strategies exist to achieve it. Several approaches involve the incorporation of a stable-isotope label using either chemical derivatization, enzymatically catalyzed incorporation of (18)O, or metabolic labeling in a cell or tissue culture. These techniques can be cost or time prohibitive or not amenable to the biological system of interest. Label-free techniques including those utilizing integrated ion abundance and spectral counting offer an alternative to stable-isotope-based methodologies. Herein, we present the comparison of stable-isotope labeling of amino acids in cell culture (SILAC) with spectral counting for the quantification of human embryonic stem cells as they differentiate toward the trophectoderm at three time points. Our spectral counting experimental strategy resulted in the identification of 2641 protein groups across three time points with an average sequence coverage of 30.3%, of which 1837 could be quantified with more than five spectral counts. SILAC quantification was able to identify 1369 protein groups with an average coverage of 24.7%, of which 1027 could be quantified across all time points. Within this context we further explore the capacity of each strategy for proteome coverage, variation in quantification, and the relative sensitivity of each technique to the detection of change in relative protein expression.
Collapse
Affiliation(s)
- Timothy S Collier
- WM Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | | | | | | |
Collapse
|
37
|
Kniemeyer O. Proteomics of eukaryotic microorganisms: The medically and biotechnologically important fungal genus Aspergillus. Proteomics 2011; 11:3232-43. [DOI: 10.1002/pmic.201100087] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/26/2011] [Accepted: 04/05/2011] [Indexed: 11/09/2022]
|
38
|
Top-Down Protein Analysis and Phylogenetic Characterization of Unsequenced Bacteria. ACTA ACUST UNITED AC 2011. [DOI: 10.1021/bk-2011-1065.ch008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
|
39
|
Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
Collapse
Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | | | | | | | | |
Collapse
|
40
|
Collier TS, Sarkar P, Franck WL, Rao BM, Dean RA, Muddiman DC. Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics. Anal Chem 2011; 82:8696-702. [PMID: 20845935 DOI: 10.1021/ac101978b] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Numerous experimental strategies exist for relative protein quantification, one of the primary objectives of mass spectrometry based proteomics analysis. These strategies mostly involve the incorporation of a stable isotope label via either metabolic incorporation in cell or tissue culture (¹⁵N/¹⁴N metabolic labeling, stable isotope labeling by amino acids in cell culture (SILAC)), chemical derivatization (ICAT, iTRAQ, TMT), or enzymatically catalyzed incorporation (¹⁸O labeling). Also, these techniques can be cost or time prohibitive or not amenable to the biological system of interest (i.e., metabolic labeling of clinical samples, most animals, or fungi). This is the case with the quantification of fungal proteomes, which often require auxotroph mutants to fully metabolically label. Alternatively, label-free strategies for protein quantification such as using integrated ion abundance and spectral counting have been demonstrated for quantification affording over 2 orders of magnitude of dynamic range which is comparable to metabolic labeling strategies. Direct comparisons of these quantitative techniques are largely lacking in the literature but are highly warranted in order to evaluate the capabilities, limitations, and analytical variability of available quantitative strategies. Here, we present the direct comparison of SILAC to label-free quantification by spectral counting of an identical set of data from the bottom-up proteomic analysis of human embryonic stem cells, which are readily able to be quantified using both strategies, finding that both strategies result in a similar number of protein identifications. We also discuss necessary constraints for accurate quantification using spectral counting and assess the potential of this label-free strategy as a viable alternative for quantitative proteomics.
Collapse
Affiliation(s)
- Timothy S Collier
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | | | | | | | | |
Collapse
|
41
|
Guan X, Yan G, Gao M, Hong G, Deng C, Zhang X. Intact-protein trapping columns for proteomic analysis in capillary high-performance liquid chromatography. J Chromatogr A 2010; 1217:6875-81. [PMID: 20870240 DOI: 10.1016/j.chroma.2010.08.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/21/2010] [Accepted: 08/20/2010] [Indexed: 11/17/2022]
Abstract
A new type of monolithic trapping columns with high mechanical strength was prepared by thin-layer sol-gel coating method and applied to trapping intact proteins for on-line capillary liquid chromatography. Monolithic trapping columns were fabricated by entrapping C8 reversed-phase particles into the capillary columns through a sol-gel network, which was formed by hydrolysis and polycondensation of methyltriethoxysilane. Hundreds times of trapping/untrapping for intact proteins were carried out. The trapping columns showed long-term stability up to 300 bar. Recovery, loading capacity and reproducibility of trapping columns were evaluated using four proteins. The recovery of four protein mixtures for the C8 monolithic trapping columns was 99.3% on average. The loading capacity of 5 mm × 320 μm i.d. C8 trapping columns for the protein mixtures was 30 μg. Day-to-day relative standard deviation (RSD) values for recoveries of protein mixtures on the same C8 trapping column ranged from 2.34 to 5.87%, column-to-column RSD values were from 3.01 to 6.81%. The C8 trapping columns were used to trap normal mouse liver intact proteins in a capillary liquid chromatography system. Results demonstrated high efficiency of the monolithic trapping columns for trapping intact proteins for proteomic analysis in on-line capillary liquid chromatography system.
Collapse
Affiliation(s)
- Xia Guan
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | | | | | | | | | | |
Collapse
|
42
|
Andrews G, Lewis D, Notey J, Kelly R, Muddiman D. Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2. Anal Bioanal Chem 2010; 398:377-89. [PMID: 20623222 PMCID: PMC3727170 DOI: 10.1007/s00216-010-3955-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/13/2010] [Accepted: 06/20/2010] [Indexed: 10/19/2022]
Abstract
The proteome of extremely thermophilic microorganisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. The secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other thermostable biomolecules that, to date, have been characterized only to a limited extent. In the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negative impact on all downstream experiments. Following efficient secretome purification, GeLC-MS(2) analysis and prediction servers suggested probable protein secretion to complement experimental data. In an effort to define the extracellular proteome of the extreme thermophilic bacterium Caldicellulosiruptor saccharolyticus, several techniques were considered regarding sample processing to achieve the most in-depth analysis of secreted proteins. Order of operation experiments, all including the C(18) bead technique, demonstrated that two levels of sample purification were necessary to effectively desalt the sample and provide sufficient protein identifications. Five sample preparation combinations yielded 71 proteins and the majority described, as enzymatic and putative uncharacterized proteins, anticipate consolidated bioprocessing applications. Nineteen proteins were predicted by Phobius, SignalP, SecretomeP, or TatP for extracellular secretion, and 11 contained transmembrane domain stretches suggested by Phobius and transmembrane hidden Markov model. The sample preparation technique demonstrating the most effective outcome for C. saccharolyticus secreted proteins in this study, involved acetone precipitation followed by the C(18) bead method in which 2.4% (63 proteins) of the predicted proteome was identified, including proteins suggested to have secretion and transmembrane moieties.
Collapse
Affiliation(s)
- Genna Andrews
- North Carolina State University, Raleigh, NC 27695, USA.
| | | | | | | | | |
Collapse
|
43
|
|
44
|
Cao J, Gonzalez-Covarrubias V, Covarrubias VM, Straubinger RM, Wang H, Duan X, Yu H, Qu J, Blanco JG. A rapid, reproducible, on-the-fly orthogonal array optimization method for targeted protein quantification by LC/MS and its application for accurate and sensitive quantification of carbonyl reductases in human liver. Anal Chem 2010; 82:2680-9. [PMID: 20218584 DOI: 10.1021/ac902314m] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Liquid chromatography (LC)/mass spectrometry (MS) in selected-reactions-monitoring (SRM) mode provides a powerful tool for targeted protein quantification. However, efficient, high-throughput strategies for proper selection of signature peptides (SP) for protein quantification and accurate optimization of their SRM conditions remain elusive. Here we describe an on-the-fly, orthogonal array optimization (OAO) approach that enables rapid, comprehensive, and reproducible SRM optimization of a large number of candidate peptides in a single nanoflow-LC/MS run. With the optimized conditions, many peptide candidates can be evaluated in biological matrixes for selection of the final SP. The OAO strategy employs a systematic experimental design that strategically varies product ions, declustering energy, and collision energy in a cycle of 25 consecutive SRM trials, which accurately reveals the effects of these factors on the signal-to-noise ratio of a candidate peptide and optimizes each. As proof of concept, we developed a highly sensitive, accurate, and reproducible method for the quantification of carbonyl reductases CBR1 and CBR3 in human liver. Candidate peptides were identified by nano-LC/LTQ/Orbitrap, filtered using a stringent set of criteria, and subjected to OAO. After evaluating both sensitivity and stability of the candidates, two SP were selected for quantification of each protein. As a result of the accurate OAO of assay conditions, sensitivities of 80 and 110 amol were achieved for CBR1 and CBR3, respectively. The method was validated and used to quantify the CBRs in 33 human liver samples. The mean level of CBR1 was 93.4 +/- 49.7 (range: 26.2-241) ppm of total protein, and of CBR3 was 7.69 +/- 4.38 (range: 1.26-17.9) ppm. Key observations of this study: (i) evaluation of peptide stability in the target matrix is essential for final selection of the SP; (ii) utilization of two unique SP contributes to high reliability of target protein quantification; (iii) it is beneficial to construct calibration curves using standard proteins of verified concentrations to avoid severe biases that may result if synthesized peptides alone are used. Overall, the OAO method is versatile and adaptable to high-throughput quantification of validated biomarkers identified by proteomic discovery experiments.
Collapse
Affiliation(s)
- Jin Cao
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, New York 14260, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Chang KY, Georgianna DR, Heber S, Payne GA, Muddiman DC. Detection of alternative splice variants at the proteome level in Aspergillus flavus. J Proteome Res 2010; 9:1209-17. [PMID: 20047314 DOI: 10.1021/pr900602d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of proteins from proteolytic peptides or intact proteins plays an essential role in proteomics. Researchers use search engines to match the acquired peptide sequences to the target proteins. However, search engines depend on protein databases to provide candidates for consideration. Alternative splicing (AS), the mechanism where the exon of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore protein variants, enable higher eukaryotic organisms, with only a limited number of genes, to have the requisite complexity and diversity at the proteome level. Multiple alternative isoforms from one gene often share common segments of sequences. However, many protein databases only include a limited number of isoforms to keep minimal redundancy. As a result, the database search might not identify a target protein even with high quality tandem MS data and accurate intact precursor ion mass. We computationally predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from 20 371 expressed sequence tags to investigate whether an alternative splicing protein database can assign a greater proportion of mass spectrometry data. The newly constructed AS database provided 9807 new alternatively spliced variants in addition to 12 832 previously annotated proteins. The searches of the existing tandem MS spectra data set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal genes appeared to have multiple protein isoforms. In addition to the discovery of splice variants, AS database also showed potential to improve genome annotation. In summary, the introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome.
Collapse
Affiliation(s)
- Kung-Yen Chang
- Bioinformatics Research Center, Center for Integrated Fungal Research, and W.M. Keck FT-ICR-MS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | | | | | | |
Collapse
|
46
|
Collier TS, Sarkar P, Rao B, Muddiman DC. Quantitative top-down proteomics of SILAC labeled human embryonic stem cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:879-889. [PMID: 20199872 DOI: 10.1016/j.jasms.2010.01.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 05/28/2023]
Abstract
Human embryonic stem cells (hESCs) are self-renewing pluripotent cells with relevance to treatment of numerous medical conditions. However, a global understanding of the role of the hESC proteome in maintaining pluripotency or triggering differentiation is still largely lacking. The emergence of top-down proteomics has facilitated the identification and characterization of intact protein forms that are not readily apparent in bottom-up studies. Combined with metabolic labeling techniques such as stable isotope labeling by amino acids in cell culture (SILAC), quantitative comparison of intact protein expression under differing experimental conditions is possible. Herein, quantitative top-down proteomics of hESCs is demonstrated using the SILAC method and nano-flow reverse phase chromatography directly coupled to a linear-ion-trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FT-ICR-MS). In this study, which to the best of our knowledge represents the first top-down analysis of hESCs, we have confidently identified 11 proteins by accurate intact mass, MS/MS, and amino acid counting facilitated by SILAC labeling. Although quantification is challenging due to the incorporation of multiple labeled amino acids (i.e., lysine and arginine) and arginine to proline conversion, we are able to quantitatively account for these phenomena using a mathematical model.
Collapse
Affiliation(s)
- Timothy S Collier
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | | | | |
Collapse
|
47
|
Zhang X, Fang A, Riley CP, Wang M, Regnier FE, Buck C. Multi-dimensional liquid chromatography in proteomics--a review. Anal Chim Acta 2010; 664:101-13. [PMID: 20363391 PMCID: PMC2852180 DOI: 10.1016/j.aca.2010.02.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/29/2010] [Accepted: 02/01/2010] [Indexed: 12/19/2022]
Abstract
Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments.
Collapse
Affiliation(s)
- Xiang Zhang
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA.
| | | | | | | | | | | |
Collapse
|
48
|
Kellie JF, Tran JC, Lee JE, Ahlf DR, Thomas HM, Ntai I, Catherman AD, Durbin KR, Zamdborg L, Vellaichamy A, Thomas PM, Kelleher NL. The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. MOLECULAR BIOSYSTEMS 2010; 6:1532-9. [PMID: 20711533 DOI: 10.1039/c000896f] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Top Down mass spectrometry (MS) has emerged as an alternative to common Bottom Up strategies for protein analysis. In the Top Down approach, intact proteins are fragmented directly in the mass spectrometer to achieve both protein identification and characterization, even capturing information on combinatorial post-translational modifications. Just in the past two years, Top Down MS has seen incremental advances in instrumentation and dedicated software, and has also experienced a major boost from refined separations of whole proteins in complex mixtures that have both high recovery and reproducibility. Combined with steadily advancing commercial MS instrumentation and data processing, a high-throughput workflow covering intact proteins and polypeptides up to 70 kDa is directly visible in the near future.
Collapse
Affiliation(s)
- John F Kellie
- Technology Development Team, Center for Top Down Proteomics, University of Illinois at Urbana-Champaign, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Garcia BA. What does the future hold for Top Down mass spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:193-202. [PMID: 19942451 DOI: 10.1016/j.jasms.2009.10.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 10/14/2009] [Accepted: 10/21/2009] [Indexed: 05/28/2023]
Abstract
Mass spectrometry (MS) research has revolutionized modern biological and biomedical fields. At the heart of the majority of mass spectrometry experiments is the use of Bottom Up mass spectrometry methods where proteins are first proteolyzed into smaller fragments before MS interrogation. The advent of electron capture dissociation and, more recently, electron-transfer dissociation, however, has allowed Top Down (analysis of intact proteins) or middle down (analysis of large polypeptides) mass spectrometry to both experience large increases in development, growth, and overall usage. Nevertheless, for high-throughput large-scale proteomic studies, Bottom Up mass spectrometry has easily dominated the field. As Top Down mass spectrometry methodology and technology continue to develop, will it genuinely be able to compete with Bottom Up mass spectrometry for whole proteome analysis? Discussed here are the current approaches, applications, issues, and future view of high-throughput Top Down mass spectrometry.
Collapse
Affiliation(s)
- Benjamin A Garcia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
| |
Collapse
|
50
|
Madsen JA, Gardner MW, Smith SI, Ledvina AR, Coon JJ, Schwartz JC, Stafford GC, Brodbelt JS. Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap. Anal Chem 2010; 81:8677-86. [PMID: 19785447 DOI: 10.1021/ac901554z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (approximately 29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest charge states), which could be useful for a priori spectral predictions and enhanced database searching for protein identification.
Collapse
Affiliation(s)
- James A Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
| | | | | | | | | | | | | | | |
Collapse
|