1
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
2
|
Villacrés C, Mizero B, Spicer V, Viner R, Saba J, Patel B, Snovida S, Jensen P, Huhmer A, Krokhin OV. Toward an Ultimate Solution for Peptide Retention Time Prediction: The Effect of Column Temperature on Separation Selectivity. J Proteome Res 2024; 23:1488-1494. [PMID: 38530092 DOI: 10.1021/acs.jproteome.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
We studied the effect of the column temperature on the selectivity of reversed-phase peptide separation in bottom-up proteomics. The number of peptide identifications from 2 h liquid chromatography with tandem mass spectrometry (LC-MS/MS) acquisitions reaches a plateau at 45-55 °C, driven simultaneously by improved separation efficiency, a gradual decrease in peptide retention, and possible on-column degradation of peptides at elevated temperatures. Performing 2D LC-MS/MS acquisitions at 25, 35, 45, and 55 °C resulted in the identification of ∼100,000 and ∼120,000 unique peptides for nonmodified and tandem mass tags (TMT)-labeled samples, respectively. These peptide collections were used to investigate the temperature-driven retention features. The latter is governed by the specific temperature response of individual residues, peptide hydrophobicity and length, and amphipathic helicity. On average, peptide retention decreased by 0.56 and 0.5% acetonitrile for each 10 °C increase for label-free and TMT-labeled peptides, respectively. This generally linear response of retention shifts allowed the extrapolation of predictive models beyond the studied temperature range. Thus, (trap) column cooling from room temperature to 0 °C will allow the retention of an additional 3% of detectable tryptic peptides. Meanwhile, the application of 90 °C would result in the loss of ∼20% of tryptic peptides that were amenable to MS/MS-based identification.
Collapse
Affiliation(s)
- Carina Villacrés
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
| | - Benilde Mizero
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Julian Saba
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Sergei Snovida
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Penny Jensen
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg R3E 3P4, Canada
| |
Collapse
|
3
|
Stastna M. Post-translational modifications of proteins in cardiovascular diseases examined by proteomic approaches. FEBS J 2024. [PMID: 38440918 DOI: 10.1111/febs.17108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024]
Abstract
Over 400 different types of post-translational modifications (PTMs) have been reported and over 200 various types of PTMs have been discovered using mass spectrometry (MS)-based proteomics. MS-based proteomics has proven to be a powerful method capable of global PTM mapping with the identification of modified proteins/peptides, the localization of PTM sites and PTM quantitation. PTMs play regulatory roles in protein functions, activities and interactions in various heart related diseases, such as ischemia/reperfusion injury, cardiomyopathy and heart failure. The recognition of PTMs that are specific to cardiovascular pathology and the clarification of the mechanisms underlying these PTMs at molecular levels are crucial for discovery of novel biomarkers and application in a clinical setting. With sensitive MS instrumentation and novel biostatistical methods for precise processing of the data, low-abundance PTMs can be successfully detected and the beneficial or unfavorable effects of specific PTMs on cardiac function can be determined. Moreover, computational proteomic strategies that can predict PTM sites based on MS data have gained an increasing interest and can contribute to characterization of PTM profiles in cardiovascular disorders. More recently, machine learning- and deep learning-based methods have been employed to predict the locations of PTMs and explore PTM crosstalk. In this review article, the types of PTMs are briefly overviewed, approaches for PTM identification/quantitation in MS-based proteomics are discussed and recently published proteomic studies on PTMs associated with cardiovascular diseases are included.
Collapse
Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
| |
Collapse
|
4
|
Wang X, Zhu T, Wang X, Peng H, Zhou G, Peng J. Preparation of two zwitterionic polymer functionalized stationary phases and comparative evaluation under mixed-mode of reversed phase/ hydrophilic interaction/ion exchange chromatography. J Chromatogr A 2024; 1714:464586. [PMID: 38118242 DOI: 10.1016/j.chroma.2023.464586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/22/2023]
Abstract
Zwitterions are a promising choice to prepare separation materials because of their hydrophilicity and biocompatibility. We described the preparation of two zwitterionic polymer functionalized stationary phases and evaluation under mixed-mode chromatography. A zwitterionic monomer, S-(4-vinylbenzyl) cysteine (SVC), was synthesized and bonded to silica via reversible addition fragmentation chain transfer (RAFT) polymerization to afford a zwitterionic stationary phase, Sil-SVC. A hydrophobic monomer, N-(4-phenylbutan-2-yl) acrylamide (NPA), was copolymerized with SVC onto the stationary phase (Sil-SVCNPA) for comparison. The stationary phases were characterized with FT-IR, TGA, EA, and zeta-potential measurements. Mobile phase composition (ACN content, pH and salt concentration) was varied to study the retention property. Linear solvation energy relationship and Van't Hoff plot were used to investigate the retention mechanism and how chromatographic conditions influenced it. Both stationary phases showed a mixed-mode of RPLC/HILIC/IEC and satisfactory performance in separating hydrophobic analytes (alkylbenzenes and polycyclic aromatic hydrocarbons), hydrophilic nucleotide and bases, and anions, high column efficiency of 60,000 plates·m-1 was achieved. In summary, zwitterionic polymers are attractive options to prepare stationary phases and the retention property can be easily regulated by copolymer.
Collapse
Affiliation(s)
- Xiang Wang
- School of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, PR China
| | - Tianrun Zhu
- Chengdu University of Technology, Yibin 644000, PR China
| | - Xingrui Wang
- School of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, PR China
| | - Huanjun Peng
- School of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, PR China
| | - Guangming Zhou
- School of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, PR China.
| | - Jingdong Peng
- School of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, PR China.
| |
Collapse
|
5
|
Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2021-mid-2023). Electrophoresis 2024; 45:165-198. [PMID: 37670208 DOI: 10.1002/elps.202300152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023]
Abstract
This review article brings a comprehensive survey of developments and applications of high-performance capillary and microchip electromigration methods (zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, micropreparation, and physicochemical characterization of peptides in the period from 2021 up to ca. the middle of 2023. Progress in the study of electromigration properties of peptides and various aspects of their analysis, such as sample preparation, adsorption suppression, electroosmotic flow regulation, and detection, are presented. New developments in the particular capillary electromigration methods are demonstrated, and several types of their applications are reported. They cover qualitative and quantitative analysis of synthetic or isolated peptides and determination of peptides in complex biomatrices, peptide profiling of biofluids and tissues, and monitoring of chemical and enzymatic reactions and physicochemical changes of peptides. They include also amino acid and sequence analysis of peptides, peptide mapping of proteins, separation of stereoisomers of peptides, and their chiral analyses. In addition, micropreparative separations and physicochemical characterization of peptides and their interactions with other (bio)molecules by the above CE methods are described.
Collapse
Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
| |
Collapse
|
6
|
Shi RL, Dillon MA, Compton PD, Sawyer WS, Thorup JR, Kwong M, Chan P, Chiu CPC, Li R, Yadav R, Lee GY, Gober JG, Li Z, ElSohly AM, Ovacik AM, Koerber JT, Spiess C, Josephs JL, Tran JC. High-Throughput Analyses of Therapeutic Antibodies Using High-Field Asymmetric Waveform Ion Mobility Spectrometry Combined with SampleStream and Intact Protein Mass Spectrometry. Anal Chem 2023; 95:17263-17272. [PMID: 37956201 DOI: 10.1021/acs.analchem.3c03158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intact protein mass spectrometry (MS) coupled with liquid chromatography was applied to characterize the pharmacokinetics and stability profiles of therapeutic proteins. However, limitations from chromatography, including throughput and carryover, result in challenges with handling large sample numbers. Here, we combined intact protein MS with multiple front-end separations, including affinity capture, SampleStream, and high-field asymmetric waveform ion mobility spectrometry (FAIMS), to perform high-throughput and specific mass measurements of a multivalent antibody with one antigen-binding fragment (Fab) fused to an immunoglobulin G1 (IgG1) antibody. Generic affinity capture ensures the retention of both intact species 1Fab-IgG1 and the tentative degradation product IgG1. Subsequently, the analytes were directly loaded into SampleStream, where each injection occurs within ∼30 s. By separating ions prior to MS detection, FAIMS further offered improvement in signal-overnoise by ∼30% for denatured protein MS via employing compensation voltages that were optimized for different antibody species. When enhanced FAIMS transmission of 1Fab-IgG1 was employed, a qualified assay was established for spiked-in serum samples between 0.1 and 25 μg/mL, resulting in ∼10% accuracy bias and precision coefficient of variation. Selective FAIMS transmission of IgG1 as the degradation surrogate product enabled more sensitive detection of clipped species for intact 1Fab-IgG1 at 5 μg/mL in serum, generating an assay to measure 1Fab-IgG1 truncation between 2.5 and 50% with accuracy and precision below 20% bias and coefficient of variation. Our results revealed that the SampleStream-FAIMS-MS platform affords high throughput, selectivity, and sensitivity for characterizing therapeutic antibodies from complex biomatrices qualitatively and quantitatively.
Collapse
Affiliation(s)
- Rachel Liuqing Shi
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Michael A Dillon
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Philip D Compton
- Integrated Protein Technologies, Evanston, Illinois 60201, United States
| | - William S Sawyer
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - John R Thorup
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Mandy Kwong
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Pamela Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Cecilia P C Chiu
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Ran Li
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, Genentech Inc., South San Francisco, California 94080, United States
| | - Rajbharan Yadav
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, Genentech Inc., South San Francisco, California 94080, United States
| | - Genee Y Lee
- Department of Molecular Oncology, Genentech Inc., South San Francisco, California 94080, United States
| | - Joshua G Gober
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | - Zhiyu Li
- The DMPK Service Department, WuXi AppTec Inc., Shanghai 200131, China
| | - Adel M ElSohly
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | - Ayse Meric Ovacik
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, Genentech Inc., South San Francisco, California 94080, United States
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Christoph Spiess
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Jonathan L Josephs
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - John C Tran
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| |
Collapse
|
7
|
Jadeja S, Kupcik R, Fabrik I, Sklenářová H, Lenčo J. A stationary phase with a positively charged surface allows for minimizing formic acid concentration in the mobile phase, enhancing electrospray ionization in LC-MS proteomic experiments. Analyst 2023; 148:5980-5990. [PMID: 37870390 DOI: 10.1039/d3an01508d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The default choice of mobile phase acidifier for bottom-up LC-MS proteomic analyses is 0.10% formic acid because of its decent acidity, decent ion pairing ability, and low suppression of electrospray ionization. In recent years, state-of-the-art columns have been designed specifically to provide efficient separation even when using an MS-friendly mobile phase of low ionic strength. Despite this, no attempts have been made to improve the sensitivity of the MS-based analytical methods by reducing the amount of formic acid in the mobile phase. In this study, we evaluated the effect of reduced formic acid concentration in the mobile phase on the chromatographic behavior and MS response of peptides when separated using columns packed with a C18 stationary phase with a positively charged surface. Using 0.01% formic acid in the mobile phase maintained excellent chromatographic performance and increased MS signal response compared to the standard of 0.10%. The enhanced MS response translated to about 50% improved peptide identifications depending on the complexity and amount of sample injected. The increased retention of peptides at a reduced formic acid concentration was directly proportional to the number of acidic residues in the peptide sequence. The study was carried out by covering a spectrum of protein samples with varied complexity using analytical flow, micro-, and nanoflow regimes to expand the applicability in routine practice.
Collapse
Affiliation(s)
- Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Rudolf Kupcik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| |
Collapse
|
8
|
Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| |
Collapse
|
9
|
Neale Q, Prefontaine A, Battellino T, Mizero B, Yeung D, Spicer V, Budisa N, Perreault H, Zahedi RP, Krokhin OV. Compendium of Chromatographic Behavior of Post-translationally and Chemically Modified Peptides in Bottom-Up Proteomic Experiments. Anal Chem 2023; 95:14634-14642. [PMID: 37739932 DOI: 10.1021/acs.analchem.3c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
We have systematically evaluated the chromatographic behavior of post-translationally/chemically modified peptides using data spanning over 70 of the most relevant modifications. These retention properties were measured for standard bottom-up proteomic settings (fully porous C18 separation media, 0.1% formic acid as ion-pairing modifier) using collections of modified/nonmodified peptide pairs. These pairs were generated by spontaneous degradation, chemical or enzymatic treatment, analysis of synthetic peptides, or the cotranslational incorporation of noncanonical proline analogues. In addition, these measurements were validated using external data acquired for synthetic peptides and enzymatically induced citrullination. Working in units of hydrophobicity index (HI, % ACN) and evaluating the average retention shifts (ΔHI) represent the simplest approach to describe the effect of modifications from a didactic point of view. Plotting HI values for modified (y-axis) vs nonmodified (x-axis) counterparts generates unique slope and intercept values for each modification defined by the chemistry of the modifying moiety: its hydrophobicity, size, pKa of ionizable groups, and position of the altered residue. These composition-dependent correlations can be used for coarse incorporation of PTMs into models for prediction of peptide retention. More accurate predictions would require the development of specific sequence-dependent algorithms to predict ΔHI values.
Collapse
Affiliation(s)
- Quinn Neale
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Alexandre Prefontaine
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Taylor Battellino
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Benilde Mizero
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Helene Perreault
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- CancerCare Manitoba Research Institute, 675 McDermot Avenue, Winnipeg R3E 0 V9, Manitoba, Canada
| | - Oleg V Krokhin
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
| |
Collapse
|
10
|
Petrosius V, Aragon-Fernandez P, Üresin N, Kovacs G, Phlairaharn T, Furtwängler B, Op De Beeck J, Skovbakke SL, Goletz S, Thomsen SF, Keller UAD, Natarajan KN, Porse BT, Schoof EM. Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition. Nat Commun 2023; 14:5910. [PMID: 37737208 PMCID: PMC10517177 DOI: 10.1038/s41467-023-41602-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-state heterogeneity and distinct cellular signaling patterns that remain obscured with population-based techniques. The limited amount of material encapsulated in a single cell however, raises significant technical challenges to molecular profiling. Due to extensive optimization efforts, single-cell proteomics by Mass Spectrometry (scp-MS) has emerged as a powerful tool to facilitate proteome profiling from ultra-low amounts of input, although further development is needed to realize its full potential. To this end, we carry out comprehensive analysis of orbitrap-based data-independent acquisition (DIA) for limited material proteomics. Notably, we find a fundamental difference between optimal DIA methods for high- and low-load samples. We further improve our low-input DIA method by relying on high-resolution MS1 quantification, thus enhancing sensitivity by more efficiently utilizing available mass analyzer time. With our ultra-low input tailored DIA method, we are able to accommodate long injection times and high resolution, while keeping the scan cycle time low enough to ensure robust quantification. Finally, we demonstrate the capability of our approach by profiling mouse embryonic stem cell culture conditions, showcasing heterogeneity in global proteomes and highlighting distinct differences in key metabolic enzyme expression in distinct cell subclusters.
Collapse
Affiliation(s)
- Valdemaras Petrosius
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Pedro Aragon-Fernandez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Nil Üresin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Gergo Kovacs
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Teeradon Phlairaharn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
- MaxPlanck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Benjamin Furtwängler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jeff Op De Beeck
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052, Gent, Belgium
| | - Sarah L Skovbakke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Simon Francis Thomsen
- Department of Dermatology, Bispebjerg Hospital and Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Kedar N Natarajan
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark.
| |
Collapse
|
11
|
Naplekov D, Jadeja S, Fučíková AM, Švec F, Sklenářová H, Lenčo J. Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection. Anal Chem 2023; 95:12339-12348. [PMID: 37565982 PMCID: PMC10448442 DOI: 10.1021/acs.analchem.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.
Collapse
Affiliation(s)
- Denis
K. Naplekov
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Alena Myslivcová Fučíková
- Department
of Biology, Faculty of Science, University
of Hradec Králové, Hradecká 1285, 500 03 Hradec Králové, Czech Republic
| | - František Švec
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Juraj Lenčo
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| |
Collapse
|
12
|
Matzinger M, Mayer RL, Mechtler K. Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing. Proteomics 2023; 23:e2200162. [PMID: 36806919 PMCID: PMC10909491 DOI: 10.1002/pmic.202200162] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/21/2023]
Abstract
The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotype. In contrast to nucleic acid sequencing, in vitro protein amplification is impossible and no single cell proteomic workflow has been established as gold standard yet. Advances in microfluidic sample preparation, multi-dimensional sample separation, sophisticated data acquisition strategies, and intelligent data analysis algorithms have resulted in major improvements to successfully analyze such tiny sample amounts with steadily boosted performance. However, among the broad variation of published approaches, it is commonly accepted that highest possible sensitivity, robustness, and throughput are still the most urgent needs for the field. While many labs have focused on multiplexing to achieve these goals, label-free SCP is a highly promising strategy as well whenever high dynamic range and unbiased accurate quantification are needed. We here focus on recent advances in label-free single-cell mass spectrometry workflows and try to guide our readers to choose the best method or combinations of methods for their specific applications. We further highlight which techniques are most propitious in the future and which applications but also limitations we foresee for the field.
Collapse
Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
| | - Rupert L. Mayer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| |
Collapse
|
13
|
Duong V, Lee H. Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:5350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
Collapse
|
14
|
Neequaye T, El Rassi Z. Poly(carboxyethyl acrylate-co-ethylene glycol dimethacrylate) precursor monolith with bonded Tris ligands for use in hydrophilic interaction capillary electrochromatography. J Chromatogr A 2023; 1695:463933. [PMID: 36966604 DOI: 10.1016/j.chroma.2023.463933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
The facile preparation of a monolithic capillary column with surface bound polar ligands for use in hydrophilic interaction capillary electrochromatography is described. It involved the conversion of poly(carboxyethyl acrylate[CEA]-co-ethylene glycol dimethacrylate[EDMA]) precursor monolith (the so-called carboxy monolith) into a Tris bonded monolith by a post-polymerization functionalization process in the presence of a water soluble carbodiimide, namely N-(3-dimethylaminopropyl)-N´-ethylcarbodiimidehydrochloride. The carbodiimide assisted conversion, allowed the covalent attachment of the carboxyl group of the precursor monolith to the amino group of the Tris ligand via a stable amide linkage. This resulted in the formation of Tris poly(CEA-co-EDMA) monolith, which exhibited the typical retention behavior of hydrophilic interaction stationary phase when analyzing polar and slightly polar neutral or charged compounds. In fact, neutral polar species such as dimethylformamide, formamide and thiourea were retained in the order of increased polarity with acetonitrile rich mobile phase. Also, neutral p-nitrophenyl maltooligosaccharides (PNP-maltooligosaccharides) served as a polar homologous series for gauging the hydrophilicity of the Tris poly(CEA-co-EDMA) monolith, thus forming a versatile testing homologous series for other hydrophilic columns. Other polar anionic species (e.g., hydroxy benzoic acids and nucleotides) and weakly polar anionic compounds (e.g., dansyl amino acids and phenoxy acid herbicides) as well as polar weak bases namely nucleobases and nucleosides were used to probe the hydrophilic characters of the Tris poly(CEA-co-EDMA) monolith. The various polar and weakly polar compounds just mentioned revealed the wide potentiality of the hydrophilic interaction column under investigation.
Collapse
|
15
|
Scrosati PM, Konermann L. Atomistic Details of Peptide Reversed-Phase Liquid Chromatography from Molecular Dynamics Simulations. Anal Chem 2023; 95:3892-3900. [PMID: 36745777 DOI: 10.1021/acs.analchem.2c05667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptide separations by reversed-phase liquid chromatography (RPLC) are an integral part of bottom-up proteomics. These separations typically employ C18 columns with water/acetonitrile gradient elution in the presence of formic acid. Despite the widespread use of such workflows, the exact nature of peptide interactions with the stationary and mobile phases is poorly understood. Here, we employ microsecond molecular dynamics (MD) simulations to uncover details of peptide RPLC. We examined two tryptic peptides, a hydrophobic and a hydrophilic species, in a slit pore lined with C18 chains that were grafted onto SiO2 support. Our simulations explored peptide trapping, followed by desorption and elution. Trapping in an aqueous mobile phase was initiated by C18 contacts with Lys butyl moieties. This was followed by extensive anchoring of nonpolar side chains (Leu/Ile/Val) in the C18 layer. Exposure to water/acetonitrile triggered peptide desorption in a stepwise fashion; charged sites close to the termini were the first to lift off, followed by the other residues. During water/acetonitrile elution, both peptides preferentially resided close to the pore center. The hydrophilic peptide exhibited no contacts with the stationary phase under these conditions. In contrast, the hydrophobic species underwent multiple transient Leu/Ile/Val binding interactions with C18 chains. These nonpolar interactions represent the foundation of differential peptide retention, in agreement with the experimental elution behavior of the two peptides. Extensive peptide/formate ion pairing was observed in water/acetonitrile, particularly at N-terminal sites. Overall, this work uncovers an unprecedented level of RPLC molecular details, paving the way for MD simulations as a future tool for improving retention prediction algorithms and for the design of novel column materials.
Collapse
Affiliation(s)
- Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| |
Collapse
|
16
|
Deberneh HM, Sadygov RG. Retention Time Alignment for Protein Turnover Studies Using Heavy Water Metabolic Labeling. J Proteome Res 2023; 22:410-419. [PMID: 36692003 PMCID: PMC10233748 DOI: 10.1021/acs.jproteome.2c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Retention time (RT) alignment has been important for robust protein identification and quantification in proteomics. In data-dependent acquisition mode, whereby the precursor ions are semistochastically chosen for fragmentation in MS/MS, the alignment is used in an approach termed matched between runs (MBR). MBR transfers peptides, which were fragmented and identified in one experiment, to a replicate experiment where they were not identified. Before the MBR transfer, the RTs of experiments are aligned to reduce the chance of erroneous transfers. Despite its widespread use in other areas of quantitative proteomics, RT alignment has not been applied in data analyses for protein turnover using an atom-based stable isotope-labeling agent such as metabolic labeling with deuterium oxide, D2O. Deuterium incorporation changes isotope profiles of intact peptides in full scans and their fragment ions in tandem mass spectra. It reduces the peptide identification rates in current database search engines. Therefore, the MBR becomes more important. Here, we report on an approach to incorporate RT alignment with peptide quantification in studies of proteome turnover using heavy water metabolic labeling and LC-MS. The RT alignment uses correlation-optimized time warping. The alignment, followed by the MBR, improves labeling time point coverage, especially for long labeling durations.
Collapse
Affiliation(s)
- Henock M. Deberneh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555
| | - Rovshan G. Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555
| |
Collapse
|