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Starovoit MR, Jadeja S, Gazárková T, Lenčo J. Mitigating In-Column Artificial Modifications in High-Temperature LC-MS for Bottom-Up Proteomics and Quality Control of Protein Biopharmaceuticals. Anal Chem 2024. [PMID: 39196537 DOI: 10.1021/acs.analchem.4c02819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Elevating the column temperature is an effective strategy for improving the chromatographic separation of peptides. However, high temperatures induce artificial modifications that compromise the quality of the peptide analysis. Here, we present a novel high-temperature LC-MS method that retains the benefits of a high column temperature while significantly reducing peptide modification and degradation during reversed-phase liquid chromatography. Our approach leverages a short inline trap column maintained at a near-ambient temperature installed upstream of a separation column. The retentivity and dimensions of the trap column were optimized to shorten the residence time of peptides in the heated separation column without compromising the separation performance. This easy-to-implement approach increased peak capacity by 1.4-fold within a 110 min peptide mapping of trastuzumab and provided 10% more peptide identifications in exploratory LC-MS proteomic analyses compared with analyses conducted at 30 °C while maintaining the extent of modifications close to the background level. In the peptide mapping of biopharmaceuticals, where in-column modifications can falsely elevate the levels of some critical quality attributes, the method reduced temperature-related artifacts by 66% for N-terminal pyroGlu and 63% for oxidized Met compared to direct injection at 60 °C, thus improving reliability in quality control of protein drugs. Our findings represent a promising advancement in LC-MS methodology, providing researchers and industry professionals with a valuable tool for improving the chromatographic separation of peptides while significantly reducing the unwanted modifications.
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Affiliation(s)
- Mykyta R Starovoit
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic
| | - Taťána Gazárková
- 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
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2
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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] [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.
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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
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3
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Van Kien N, Jeong YH, Seog DJH, Ryoo JJ. Mechanistic study of ultrasound-assisted chromatography using plastic and stainless steel columns. J Chromatogr A 2023; 1710:464402. [PMID: 37797422 DOI: 10.1016/j.chroma.2023.464402] [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: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Based on the previous ultrasound-assisted chromatography (UAC) studies on plastic and stainless steel (SS) columns, this study explores the UAC mechanism by comparatively analyzing ultrasound effects on plastic and SS columns with C18 stationary phase when separating a mixture of polycyclic aromatic hydrocarbons (PAHs) under various ultrasound intensities. The results showed a substantial difference in H values between the PEEK and SS columns under the influence of ultrasound agitation. Specifically, for the pyrene peak, as the ultrasonic intensity increased from 0% to 100% of 900 W, the H values of the SS column slightly rose from 8.82 μm to 9.86 μm. Conversely, the corresponding values for the PEEK column exhibited a significant 12-fold increase from 11.5 μm to 134 μm. The findings demonstrated poor penetration of ultrasound energy through the SS column, and the temperature rise of the medium induced by the ultrasound was the primary contributing factor to PAH separation. However, ultrasound easily penetrated through the plastic column, resulting in acoustic cavitation within the C18 polyether ether ketone (PEEK) column. Cavitation induced heat generation and contributed to a decrease in retention time and the magnitude of peak broadening or distortion, depending on the specific ultrasonic energy. Based on the estimated change in inlet temperature of the PEEK column due to an acoustic effect, the comparison with temperature effects under non-sonic conditions consistently demonstrated a stronger acoustic effect in reducing the retention time, by 2-9%, depending on specific peaks and pairs. We revisited the previously described separation mechanism of ultrasound-assisted ion chromatography and conjoined with our findings to infer and establish a thorough explanation for the previously unexplained separation mechanism of chiral separation and size exclusion chromatography by UAC using SS columns.
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Affiliation(s)
- Nguyen Van Kien
- Department of Chemistry Education, Kyungpook National University, Daegu, 702-701, the Republic of Korea South Korea
| | - Young Han Jeong
- Department of Chemistry Education, Kyungpook National University, Daegu, 702-701, the Republic of Korea South Korea
| | - David Jin Han Seog
- Department of Chemistry Education, Kyungpook National University, Daegu, 702-701, the Republic of Korea South Korea
| | - Jae Jeong Ryoo
- Department of Chemistry Education, Kyungpook National University, Daegu, 702-701, the Republic of Korea South Korea.
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4
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Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022; 21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Denis K Naplekov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Oleg V Krokhin
- Department of Internal Medicine, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, WinnipegR3E 3P4, Manitoba, Canada
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Jiří Urban
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Ken Broeckhoven
- Department of Chemical Engineering (CHIS), Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050Brussel, Belgium
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
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5
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Jin C, Mo Y, Zhao L, Xiao Z, Zhu S, He Z, Chen Z, Zhang M, Shu L, Qiu R. Host-Endosymbiont Relationship Impacts the Retention of Bacteria-Containing Amoeba Spores in Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12347-12357. [PMID: 35916900 DOI: 10.1021/acs.est.2c02899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Amoebae are protists that are commonly found in water, soil, and other habitats around the world and have complex interactions with other microorganisms. In this work, we investigated how host-endosymbiont interactions between amoebae and bacteria impacted the retention behavior of amoeba spores in porous media. A model amoeba species, Dictyostelium discoideum, and a representative bacterium, Burkholderia agricolaris B1qs70, were used to prepare amoeba spores that carried bacteria. After interacting with B. agricolaris, the retention of D. discoideum spores was enhanced compared to noninfected spores. Diverse proteins, especially proteins contributing to the looser exosporium structure and cell adhesion functionality, are secreted in higher quantities on the exosporium surface of infected spores compared to that of noninfected ones. Comprehensive examinations using a quartz crystal microbalance with dissipation (QCM-D), a parallel plate chamber, and a single-cell force microscope present coherent evidence that changes in the exosporium of D. discoideum spores due to infection by B. agricolaris enhance the connections between spores in the suspension and the spores that were previously deposited on the collector surface, thus resulting in more retention compared to the uninfected ones in porous media. This work provides novel insight into the retention of amoeba spores after bacterial infection in porous media and suggests that the host-endosymbiont relationship regulates the fate of biocolloids in drinking water systems, groundwater, and other porous environments.
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Affiliation(s)
- Chao Jin
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yijun Mo
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Lingan Zhao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Zihan Xiao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Shishu Zhu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Zhenzhen He
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Zijian Chen
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Miaoyue Zhang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Longfei Shu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, P. R. China
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6
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Eun DB, Jeong YH, Ryoo JJ. Improvement of chiral separation efficiency through temperature control during one time high performance liquid chromatography analysis. Chirality 2022; 34:941-947. [PMID: 35352403 DOI: 10.1002/chir.23444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/15/2022] [Indexed: 11/07/2022]
Abstract
This study examined how manual temperature control affects the separation of two enantiomers of five racemic mixtures using high-performance liquid chromatography (HPLC) in terms of separation factor (α), resolution (Rs), and the number of theoretical plates (N). The results showed that heating/cooling during one time HPLC analysis improved the separation factor and resolution.
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Affiliation(s)
- Dan Bi Eun
- Department of Chemistry Education, Kyungpook Nat'l Univ. Daegu, South Korea
| | - Young Han Jeong
- Department of Chemistry, Kyungpook Nat'l Univ. Daegu, South Korea
| | - Jae Jeong Ryoo
- Department of Chemistry Education, Kyungpook Nat'l Univ. Daegu, South Korea
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7
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CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides. Mol Cell Proteomics 2021; 20:100170. [PMID: 34740827 PMCID: PMC8646264 DOI: 10.1016/j.mcpro.2021.100170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
Reversed-phase solid-phase extraction (SPE) techniques are commonly used for desalting samples before LC/MS/MS in shotgun proteomics. However, hydrophilic peptides are often lost during the desalting step under the standard SPE conditions. Here, we describe a simple protocol in which a stop-and-go extraction tip packed with a poly(styrene-divinylbenzene) copolymer disc is used at 4 °C during sample loading without any organic solvent. Using this method, which we designate as the CoolTip protocol, we identified 2.9-fold more tryptic peptides and 6.1-fold more tryptic phosphopeptides from HeLa lysates than the standard SPE protocol for hydrophilic peptides, with a mobile phase of less than 8% acetonitrile in LC/MS/MS. There was no decrease in the recovery of hydrophobic peptides. CoolTip also provided better quantitative reproducibility in LC/MS/MS analysis. We anticipate that this protocol will provide improved performance in many kinds of shotgun proteomics experiments. CoolTip, a StageTip with a poly(styrene-divinylbenzene) disc operated at 4 °C. Identification of more 6.1-fold hydrophilic phosphopeptides from HeLa lysates. No decrease in the recovery of hydrophobic peptides using the CoolTip protocol. Better reproducibility in quantitative LC/MS/MS analysis.
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8
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Yin L, Huang Y, Wang C, Dong H, Ding Y, Huang B, Wu J. Development of a Novel and Stability Indicating RP-HPLC-UV Method for Simultaneous Analysis of Carbetocin and Ten Impurities in Carbetocin Injection Products. Chromatographia 2021. [DOI: 10.1007/s10337-021-04083-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Gussakovsky D, Anderson G, Spicer V, Krokhin OV. Peptide separation selectivity in proteomics LC-MS experiments: Comparison of formic and mixed formic/heptafluorobutyric acids ion-pairing modifiers. J Sep Sci 2020; 43:3830-3839. [PMID: 32818315 DOI: 10.1002/jssc.202000578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Separation selectivity and detection sensitivity of reversed-phase high-performance liquid chromatography with tandem mass spectrometry analyses were compared for formic (0.1%) and formic/heptafluorobutyric (0.1%/0.005%) acid based eluents using a proteomic data set of ∼12 000 paired peptides. The addition of a small amount of hydrophobic heptafluorobutyric acid ion-pairing modifier increased peptide retention by up to 10% acetonitrile depending on peptide charge, size, and hydrophobicity. Retention increase was greatest for peptides that were short, highly charged, and hydrophilic. There was an ∼3.75-fold reduction in MS signal observed across the whole population of peptides following the addition of heptafluorobutyric acid. This resulted in ∼36% and ∼21% reduction of detected proteins and unique peptides for the whole cell lysate digests, respectively. We also confirmed that the separation selectivity of the formic/heptafluorobutyric acid system was very similar to the commonly used conditions of 0.1% trifluoroacetic acid, and developed a new version of the Sequence-Specific Retention calculator model for the formic/heptafluorobutyric acid system showing the same ∼0.98 R2 -value accuracy as the Sequence-Specific Retention calculator formic acid model. In silico simulation of peptide distribution in separation space showed that the addition of 0.005% heptafluorobutyric acid to the 0.1% formic acid system increased potential proteome coverage by ∼11% of detectable species (tryptic peptides ≥ four amino acids).
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Affiliation(s)
- Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Geoff Anderson
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vic Spicer
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada.,Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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10
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Tsai CF, Smith JS, Krajewski K, Zhao R, Moghieb AM, Nicora CD, Xiong X, Moore RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S, Shi T. Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides. Anal Chem 2019; 91:11606-11613. [PMID: 31418558 PMCID: PMC7197904 DOI: 10.1021/acs.analchem.9b01814] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein phosphorylation is a critical post-translational modification (PTM). Despite recent technological advances in reversed-phase liquid chromatography (RPLC)-mass spectrometry (MS)-based proteomics, comprehensive phosphoproteomic coverage in complex biological systems remains challenging, especially for hydrophilic phosphopeptides with enriched regions of serines, threonines, and tyrosines that often orchestrate critical biological functions. To address this issue, we developed a simple, easily implemented method to introduce a commonly used tandem mass tag (TMT) to increase peptide hydrophobicity, effectively enhancing RPLC-MS analysis of hydrophilic peptides. Different from conventional TMT labeling, this method capitalizes on using a nonprimary amine buffer and TMT labeling occurring before C18-based solid phase extraction. Through phosphoproteomic analyses of MCF7 cells, we have demonstrated that this method can greatly increase the number of identified hydrophilic phosphopeptides and improve MS detection signals. We applied this method to study the peptide QPSSSR, a very hydrophilic tryptic peptide located on the C-terminus of the G protein-coupled receptor (GPCR) CXCR3. Identification of QPSSSR has never been reported, and we were unable to detect it by traditional methods. We validated our TMT labeling strategy by comparative RPLC-MS analyses of both a hydrophilic QPSSSR peptide library as well as common phosphopeptides. We further confirmed the utility of this method by quantifying QPSSSR phosphorylation abundances in HEK 293 cells under different treatment conditions predicted to alter QPSSSR phosphorylation. We anticipate that this simple TMT labeling method can be broadly used not only for decoding GPCR phosphoproteome but also for effective RPLC-MS analysis of other highly hydrophilic analytes.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jeffrey S. Smith
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599,United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ahmed M. Moghieb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xinyu Xiong
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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11
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Rerick MT, Groskreutz SR, Weber SG. Multiplicative On-Column Solute Focusing Using Spatially Dependent Temperature Programming for Capillary HPLC. Anal Chem 2019; 91:2854-2860. [DOI: 10.1021/acs.analchem.8b04826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Michael T. Rerick
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stephen R. Groskreutz
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stephen G. Weber
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Brunet MA, Levesque SA, Hunting DJ, Cohen AA, Roucou X. Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome Res 2018; 28:609-624. [PMID: 29626081 PMCID: PMC5932603 DOI: 10.1101/gr.230938.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts. This has important consequences for the correlation of phenotypes and genotypes. Most alternative ORFs are not yet annotated because of a lack of evidence, and this absence from databases precludes their detection by standard proteomic methods, such as mass spectrometry. Here, we demonstrate how current approaches tend to overlook alternative ORFs, hindering the discovery of new genetic drivers and fundamental research. We discuss available tools and techniques to improve identification of proteins from alternative ORFs and finally suggest a novel annotation system to permit a more complete representation of the transcriptomic and proteomic information contained within a gene. Given the crucial challenge of distinguishing functional ORFs from random ones, the suggested pipeline emphasizes both experimental data and conservation signatures. The addition of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current genome annotations and thus permit their inclusion in hypotheses and models, which relate phenotypes and genotypes.
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Affiliation(s)
- Marie A Brunet
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
| | - Sébastien A Levesque
- Pediatric Department, Centre Hospitalier de l'Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Darel J Hunting
- Department of Nuclear Medicine & Radiobiology, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Alan A Cohen
- Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada
| | - Xavier Roucou
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
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