1
|
Menneteau T, Saveliev S, Butré CI, Rivera AKG, Urh M, Delobel A. Addressing common challenges of biotherapeutic protein peptide mapping using recombinant trypsin. J Pharm Biomed Anal 2024; 243:116124. [PMID: 38520959 DOI: 10.1016/j.jpba.2024.116124] [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: 02/09/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
Peptide mapping is the key method for characterization of primary structure of biotherapeutic proteins. This method relies on digestion of proteins into peptides that are then analyzed for amino acid sequence and post-translational modifications. Owing to its high activity and cleavage specificity, trypsin is the protease of choice for peptide mapping. In this study, we investigated critical requirements of peptide mapping and how trypsin affects these requirements. We found that the commonly used MS-grade trypsins contained non-specific, chymotryptic-like cleavage activity causing generation of semi-tryptic peptides and degradation of tryptic-specific peptides. Furthermore, MS-grade trypsins contained pre-existing autoproteolytic peptides and, moreover, additional autoproteolytic peptides were resulting from prominent autoproteolysis during digestion. In our long-standing quest to improve trypsin performance, we developed novel recombinant trypsin and evaluated whether it could address major trypsin drawbacks in peptide mapping. The study showed that the novel trypsin was free of detectable non-specific cleavage activity, had negligible level of autoproteolysis and maintained high activity over the course of digestion reaction. Taking advantage of the novel trypsin advanced properties, especially high cleavage specificity, we established the application for use of large trypsin quantities to digest proteolytically resistant protein sites without negative side effects. We also tested trypsin/Lys-C mix comprising the novel trypsin and showed elimination of non-specific cleavages observed in the digests with the commonly used trypsins. In addition, the improved features of the novel trypsin allowed us to establish the method for accurate and efficient non-enzymatic PTM analysis in biotherapeutic proteins.
Collapse
Affiliation(s)
- Thomas Menneteau
- Quality Assistance SA, Technoparc de Thudinie 2, Donstiennes 6536, Belgium
| | - Sergei Saveliev
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, United States
| | - Claire I Butré
- Quality Assistance SA, Technoparc de Thudinie 2, Donstiennes 6536, Belgium
| | | | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, United States
| | - Arnaud Delobel
- Quality Assistance SA, Technoparc de Thudinie 2, Donstiennes 6536, Belgium.
| |
Collapse
|
2
|
Yildiz P, Ozcan S. A single protein to multiple peptides: Investigation of protein-peptide correlations using targeted alpha-2-macroglobulin analysis. Talanta 2023; 265:124878. [PMID: 37392709 DOI: 10.1016/j.talanta.2023.124878] [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: 01/23/2023] [Revised: 04/30/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023]
Abstract
Recent advances in proteomics technologies have enabled the analysis of thousands of proteins in a high-throughput manner. Mass spectrometry (MS) based proteomics uses a peptide-centric approach where biological samples undergo specific proteolytic digestion and then only unique peptides are used for protein identification and quantification. Considering the fact that a single protein may have multiple unique peptides and a number of different forms, it becomes essential to understand dynamic protein-peptide relationships to ensure robust and reliable peptide-centric protein analysis. In this study, we investigated the correlation between protein concentration and corresponding unique peptide responses under a conventional proteolytic digestion condition. Protein-peptide correlation, digestion efficiency, matrix-effect, and concentration-effect were evaluated. Twelve unique peptides of alpha-2-macroglobulin (A2MG) were monitored using a targeted MS approach to acquire insights into protein-peptide dynamics. Although the peptide responses were reproducible between replicates, protein-peptide correlation was moderate in protein standards and low in complex matrices. The results suggest that reproducible peptide signal could be misleading in clinical studies and a peptide selection could dramatically change the outcome at protein level. This is the first study investigating quantitative protein-peptide correlations in biological samples using all unique peptides representing the same protein and opens a discussion on peptide-based proteomics.
Collapse
Affiliation(s)
- Pelin Yildiz
- Department of Chemistry, Middle East Technical University (METU), 06800, Ankara, Turkiye; Nanografi Nanotechnology Co, Middle East Technical University (METU) Technopolis, 06531, Ankara, Turkiye
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University (METU), 06800, Ankara, Turkiye; Cancer Systems Biology Laboratory (CanSyL), Middle East Technical University (METU), 06800, Ankara, Turkiye.
| |
Collapse
|
3
|
Nickerson JL, Doucette AA. Maximizing Cumulative Trypsin Activity with Calcium at Elevated Temperature for Enhanced Bottom-Up Proteome Analysis. BIOLOGY 2022; 11:biology11101444. [PMID: 36290348 PMCID: PMC9598648 DOI: 10.3390/biology11101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Simple Summary Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Abstract Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.
Collapse
|
4
|
Rezaee N, Hasanvand P, Bagheri Lotfabad T, Heydarinasab A, Khodabandeh M, Yaghmaei S. Study on the use of bovine blood protein hydrolysate as a peptone in microbial culture media. Prep Biochem Biotechnol 2022:1-12. [DOI: 10.1080/10826068.2022.2119577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Nasim Rezaee
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Pedram Hasanvand
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Tayebe Bagheri Lotfabad
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Amir Heydarinasab
- Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mahvash Khodabandeh
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Soheila Yaghmaei
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| |
Collapse
|
5
|
Ai Y, Xu J, Gunawardena HP, Zare RN, Chen H. Investigation of Tryptic Protein Digestion in Microdroplets and in Bulk Solution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1238-1249. [PMID: 35647885 PMCID: PMC10512443 DOI: 10.1021/jasms.2c00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent studies have shown that ultrafast enzymatic digestion of proteins can be achieved in microdroplet within 250 μs. Further investigation of peptides resulting from microdroplet digestion (MD) would be necessary to evaluate it as an alternative to the conventional bulk digestion for bottom-up and biotherapeutic protein characterization. Herein we examined and compared protein tryptic digestion in both MD and bulk solution. In the case of MD of β-lactoglobulin B, the preservation of long peptides was observed due to the short digestion time. In addition, MD is applicable to digest both high- and low-abundance proteins in mixture. In the case of digesting NIST 8671 mAb antibody containing a low level of commonly encountered host cell protein (HCP) PLBL2 (mAb:PLBL2 = 100:1 by weight), MD produced lower levels of digestion-induced chemical modifications of asparagine/glutamine deamidation, compared with overnight digestion. No significant difference between MD and bulk digestion was observed in terms of trypsin digestion specificity based on examination of semi- and unspecific-cleaved peptides. Our study suggests that MD, a fast digestion approach, could be adopted for bottom-up proteomics research and for peptide mapping of mAbs to characterize site-specific deamidation and glycosylation, for the purpose of development of biopharmaceuticals.
Collapse
Affiliation(s)
- Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Jeffrey Xu
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Harsha P. Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, USA
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| |
Collapse
|
6
|
High voltage electrical treatments can eco-efficiently promote the production of high added value peptides during chymotryptic hydrolysis of β-lactoglobulin. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
7
|
Gregersen S, Kongsted ASH, Nielsen RB, Hansen SS, Lau FA, Rasmussen JB, Holdt SL, Jacobsen C. Enzymatic extraction improves intracellular protein recovery from the industrial carrageenan seaweed Eucheuma denticulatum revealed by quantitative, subcellular protein profiling: A high potential source of functional food ingredients. Food Chem X 2021; 12:100137. [PMID: 34746746 PMCID: PMC8554166 DOI: 10.1016/j.fochx.2021.100137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 01/13/2023] Open
Abstract
Seaweeds are regarded as a sustainable source of food protein, but protein extraction is severely impaired by the complex extracellular matrix. In this work, we investigated the protein-level effects of enzymatic extraction upstream of carrageenan extraction for the industrial red seaweed Eucheuma denticulatum. Combination of quantitative proteomics and bioinformatic prediction of subcellular localization was shown to have immense potential for process evaluation; even in the case of poorly annotated species such as E. denticulatum. Applying cell wall degrading enzymes markedly improved the relative recovery of intracellular proteins compared to treatment with proteolytic enzymes or no enzymatic treatment. Moreover, results suggest that proteomics data may prove useful for characterizing amino acid composition and that length-normalization is a viable approach for relative protein quantification in non-specific analysis. Importantly, the extracts were abundant in proteins, which contained both previously verified and novel, potential bioactive peptides, highlighting their potential for application as functional food ingredients.
Collapse
Affiliation(s)
- Simon Gregersen
- Department of Chemistry and Bioscience, Aalborg University, Denmark
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Reinders LMH, Klassen MD, Teutenberg T, Jaeger M, Schmidt TC. Development of a multidimensional online method for the characterization and quantification of monoclonal antibodies using immobilized flow-through enzyme reactors. Anal Bioanal Chem 2021; 413:7119-7128. [PMID: 34628527 DOI: 10.1007/s00216-021-03683-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 01/06/2023]
Abstract
Complete characterization and quantification of monoclonal antibodies often rely on enzymatic digestion with trypsin. In order to accelerate and automate this frequently performed sample preparation step, immobilized enzyme reactors (IMER) compatible with standard HPLC systems were used. This allows an automated online approach in all analytical laboratories. We were able to demonstrate that the required digestion time for the model monoclonal antibody rituximab could be reduced to 20 min. Nevertheless, a previous denaturation of the protein is required, which also needs 20 min. Recoveries were determined at various concentrations and were 100% ± 1% at 100 ng on column, 96% ± 7% at 250 ng on column and 98% ± 2% at 450 ng on column. Despite these good recoveries, complete digestion was not achieved, resulting in a poorer limit of quantification. This is 50 ng on column under optimized IMER conditions, whereas an offline digest on the same system achieved 0.3 ng on column. Furthermore, our work revealed that TRIS buffers, when used with an IMER system, led to alteration of the peptides and induced modifications in the peptides. Therefore, the addition of TRIS should be avoided when working at elevated temperatures of about 60 °C. Nevertheless, our results have shown that the recovery is not significantly influenced whether TRIS is used or not (recovery: 96 ± 7% with TRIS vs. 100 ± 9% without TRIS).
Collapse
Affiliation(s)
- Lars M H Reinders
- Institut für Energie und Umwelttechnik e. V. (IUTA, Institute of Energy and Environmental Technology), Bliersheimer Str. 58-60, 47229, Duisburg, Germany.,Hochschule Niederrhein, University of Applied Science, Reinarzstr. 49, 47805, Krefeld, Germany.,Faculty of Chemistry, Instrumental Analytical Chemistry, University Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Martin D Klassen
- Institut für Energie und Umwelttechnik e. V. (IUTA, Institute of Energy and Environmental Technology), Bliersheimer Str. 58-60, 47229, Duisburg, Germany
| | - Thorsten Teutenberg
- Institut für Energie und Umwelttechnik e. V. (IUTA, Institute of Energy and Environmental Technology), Bliersheimer Str. 58-60, 47229, Duisburg, Germany.
| | - Martin Jaeger
- Hochschule Niederrhein, University of Applied Science, Reinarzstr. 49, 47805, Krefeld, Germany
| | - Torsten C Schmidt
- Faculty of Chemistry, Instrumental Analytical Chemistry, University Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| |
Collapse
|
9
|
Ieritano C, Rickert D, Featherstone J, Honek JF, Campbell JL, Blanc JCYL, Schneider BB, Hopkins WS. The Charge-State and Structural Stability of Peptides Conferred by Microsolvating Environments in Differential Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:956-968. [PMID: 33733774 DOI: 10.1021/jasms.0c00469] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of solvent vapor in a differential mobility spectrometry (DMS) cell creates a microsolvating environment that can mitigate complications associated with field-induced heating. In the case of peptides, the microsolvation of protonation sites results in a stabilization of charge density through localized solvent clustering, sheltering the ion from collisional activation. Seeding the DMS carrier gas (N2) with a solvent vapor prevented nearly all field-induced fragmentation of the protonated peptides GGG, AAA, and the Lys-rich Polybia-MP1 (IDWKKLLDAAKQIL-NH2). Modeling the microsolvation propensity of protonated n-propylamine [PrNH3]+, a mimic of the Lys side chain and N-terminus, with common gas-phase modifiers (H2O, MeOH, EtOH, iPrOH, acetone, and MeCN) confirms that all solvent molecules form stable clusters at the site of protonation. Moreover, modeling populations of microsolvated clusters indicates that species containing protonated amine moieties exist as microsolvated species with one to six solvent ligands at all effective ion temperatures (Teff) accessible during a DMS experiment (ca. 375-600 K). Calculated Teff of protonated GGG, AAA, and Polybia-MPI using a modified two-temperature theory approach were up to 86 K cooler in DMS environments seeded with solvent vapor compared to pure N2 environments. Stabilizing effects were largely driven by an increase in the ion's apparent collision cross section and by evaporative cooling processes induced by the dynamic evaporation/condensation cycles incurred in the presence of an oscillating electric separation field. When the microsolvating partner was a protic solvent, abstraction of a proton from [MP1 + 3H]3+ to yield [MP1 + 2H]2+ was observed. This result was attributed to the proclivity of protic solvents to form hydrogen-bond networks with enhanced gas-phase basicity. Collectively, microsolvation provides analytes with a solvent "air bag," whereby charge reduction and microsolvation-induced stabilization were shown to shelter peptides from the fragmentation induced by field heating and may play a role in preserving native-like ion configurations.
Collapse
Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Daniel Rickert
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Joshua Featherstone
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Watermine Innovation, Waterloo N0B 2T0, Ontario, Canada
- Bedrock Scientific, Milton L6T 6J9, Ontario, Canada
| | | | | | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Watermine Innovation, Waterloo N0B 2T0, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong
| |
Collapse
|
10
|
Rolfs Z, Millikin RJ, Smith LM. An Algorithm to Improve the Speed of Semi and Non-Specific Enzyme Searches in Proteomics. Curr Bioinform 2021; 15:1065-1074. [PMID: 33692656 DOI: 10.2174/1574893615999200429123334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background The identification of non-specifically cleaved peptides in proteomics and peptidomics poses a significant computational challenge. Current strategies for the identification of such peptides are typically time consuming and hinder routine data analysis. Objective We aimed to design an algorithm that would improve the speed of semi- and non-specific enzyme searches and could be applicable to existing search programs. Method We developed a novel search algorithm that leverages fragment-ion redundancy to simultaneously search multiple non-specifically cleaved peptides at once. Briefly, a theoretical peptide tandem mass spectrum is generated using only the fragment-ion series from a single terminus. This spectrum serves as a proxy for several shorter theoretical peptides sharing the same terminus. After database searching, amino acids are removed from the opposing terminus until the observed and theoretical precursor masses match within a given mass tolerance. Results The algorithm was implemented in the search program MetaMorpheus and found to perform an order of magnitude faster than the traditional MetaMorpheus search and produce superior results. Conclusion We report a speedy non-specific enzyme search algorithm which is open-source and enables search programs to utilize fragment-ion redundancy to achieve a notable increase in search speed.
Collapse
Affiliation(s)
- Zach Rolfs
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
11
|
Nonspecific cleavages arising from reconstitution of trypsin under mildly acidic conditions. PLoS One 2020; 15:e0236740. [PMID: 32722706 PMCID: PMC7386593 DOI: 10.1371/journal.pone.0236740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/13/2020] [Indexed: 11/19/2022] Open
Abstract
Tryptic digestion of proteins followed by liquid chromatography with tandem mass spectrometry analysis is an extensively used approach in proteomics research and biopharmaceutical product characterization, owing to the high level of cleavage fidelity produced with this technique. However, nonspecific trypsin cleavages have been frequently reported and shown to be related to a number of digestion conditions and predigestion sample treatments. In this work, we reveal that, for a number of commercial trypsins, reconstitution and storage conditions can have a significant impact on the occurrence of trypsin nonspecific cleavages. We analyzed the tryptic digestion of a variety of biotherapeutics, using trypsins reconstituted under different conditions. The results indicate that, for many commercial trypsins, commonly recommended reconstitution/storage conditions (mildly acidic, e.g., 50 mM acetic acid, 1 mM HCl) can actually promote nonspecific trypsin activities, which are time dependent and can be as high as 20% in total relative abundance. In contrast, using water for reconstitution and storage can effectively limit nonspecific cleavages to 1%. Interestingly, the performances of different commercial trypsins were found to be quite distinct in their levels of nonspecific cleavages and responses to the two reconstitution conditions. Our findings demonstrate the importance of choosing the appropriate trypsin for tryptic digestion and the necessity of assessing the impact of trypsin reconstitution and storage on nonspecific cleavages. We advocate for manufacturers of commercial trypsins to reevaluate manufacturing processes and reconstitution/storage conditions to provide good cleavage specificity.
Collapse
|
12
|
Lin Z, Ren Y, Shi Z, Zhang K, Yang H, Liu S, Hao P. Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8733. [PMID: 32031715 DOI: 10.1002/rcm.8733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
UNLABELLED High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation. METHODS In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry. RESULTS Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol. CONCLUSIONS The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol.
Collapse
Affiliation(s)
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhaomei Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| |
Collapse
|
13
|
Prandi B, Lambertini F, Varani M, Faccini A, Suman M, Leporati A, Tedeschi T, Sforza S. Assessment of Enzymatic Improvers in Flours Using LC-MS/MS Detection of Marker Tryptic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:240-248. [PMID: 32031395 DOI: 10.1021/jasms.9b00109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enzymatic improvers are enzymes obtained from microbial or fungal cultures, added as technical adjuvants to flour, with the aim of improving the dough characteristics in bakery products. They are used in a low ppm range and, being technical adjuvants, can go undeclared on the label. Many types of enzymatic improvers are present on the market, such as amylases, lipases, proteases, xylanases, glucose oxidases, and others, each with a different function. Analytical methods capable of detecting these enzymes are needed, particularly for bakery companies, in order to monitor the quality of raw materials and to detect any undeclared presence. In the present work, specific peptide markers, obtained by enzymatic digestion, have been used to detect the presence of enzymatic improvers by LC-MS/MS techniques. Promising results were obtained for some enzymes acting on the carbohydrate fraction (glucoamylase, glucose oxidase, xylanase) in which amounts as low as 20 ppm could be identified in blind flour samples. For lipases and proteases the method proved to be very effective in terms of specific identification, even if less sensitive.
Collapse
Affiliation(s)
- Barbara Prandi
- Department of Food and Drug , University of Parma , Parco Area delle Scienze 27/A , 43124 Parma , Italy
- Department of Human Sciences and Quality of Life Promotion , Telematic University San Raffaele Roma , via Val Cannuta 247 , 00166 Rome , Italy
| | - Francesca Lambertini
- Advanced Research Laboratory , Barilla G.R. F.lli SpA , via Mantova 166 , 43122 Parma , Italy
| | - Martina Varani
- Department of Food and Drug , University of Parma , Parco Area delle Scienze 27/A , 43124 Parma , Italy
| | - Andrea Faccini
- Interdepartmental Centre for Measurements , University of Parma , Parco Area delle Scienze 23/A , 43124 Parma , Italy
| | - Michele Suman
- Advanced Research Laboratory , Barilla G.R. F.lli SpA , via Mantova 166 , 43122 Parma , Italy
| | - Andrea Leporati
- Advanced Research Laboratory , Barilla G.R. F.lli SpA , via Mantova 166 , 43122 Parma , Italy
| | - Tullia Tedeschi
- Department of Food and Drug , University of Parma , Parco Area delle Scienze 27/A , 43124 Parma , Italy
| | - Stefano Sforza
- Department of Food and Drug , University of Parma , Parco Area delle Scienze 27/A , 43124 Parma , Italy
| |
Collapse
|
14
|
Fang P, Xie J, Sang S, Zhang L, Liu M, Yang L, Xu Y, Yan G, Yao J, Gao X, Qian W, Wang Z, Zhang Y, Yang P, Shen H. Multilayered N-Glycoproteome Profiling Reveals Highly Heterogeneous and Dysregulated Protein N-Glycosylation Related to Alzheimer’s Disease. Anal Chem 2019; 92:867-874. [PMID: 31751117 DOI: 10.1021/acs.analchem.9b03555] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - JuanJuan Xie
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Shaoming Sang
- Department of Neurology, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science & Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mingqi Liu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lujie Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yiteng Xu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xing Gao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenjing Qian
- Department of Neurology, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science & Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Zhongfeng Wang
- Department of Neurology, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science & Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huali Shen
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| |
Collapse
|
15
|
Wu HY, Ma MC, Pan YY, Shih CL, Zgoda V, Li CS, Lin LC, Liao PC. Assessing the Similarity between Random Copolymer Drug Glatiramer Acetate by Using LC-MS Data Coupling with Hypothesis Testing. Anal Chem 2019; 91:14281-14289. [PMID: 31590482 DOI: 10.1021/acs.analchem.9b02488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The full characterization of nonbiological complex drugs (NBCDs) is not possible, but analytical approaches are of urgent need to evaluate the similarity between different lots and compare with their follow-up versions. Here, we propose a hypothesis testing-based approach to assess the similarity/difference between random amino acid copolymer drugs using liquid chromatography mass spectrometry (LC-MS) analysis. Two glatiramer acetate (GA) drugs, commercially available Copaxone and in-house synthesized SPT, and a negative control were digested by Lys-C and followed by HILIC-MS analysis. After retention time alignment and feature identification, 1627 features matched to m/z values in an elemental composition database were considered as derived from active drug ingredients. A hypothesis testing approach, the sum of squared deviations test, was developed to process high-dimensional data derived from LC-MS spectra. The feasibility of this approach was first demonstrated by testing 5 versus 5 lots of Copaxone and Copaxone versus SPT, which suggested a significant similarity by obtaining the estimated 95th percentile of the distribution of the estimator (ρ̂(95%)) at 0.0056 (p-value = 0.0026) and 0.0026 (p-value < 0.0001), respectively. In contrast, the ρ̂ was 0.036 (p-value = 1.00), while comparing Copaxone and the negative control, implying a lack of similarity. We further synthesized nine stable isotope-labeled peptides to validate the proposed amino acid sequences in the database, demonstrating the correctness in sequence identification. The quantitation variations in our analytical procedures were determined to be 6.8-7.7%. This approach was found to have a great potential for evaluating the similarity between generic NBCDs and listed reference drugs, as well as to monitor the lot-to-lot variation.
Collapse
Affiliation(s)
- Hsin-Yi Wu
- Instrumentation Center , National Taiwan University , Taipei 106 , Taiwan
| | - Mi-Chia Ma
- Department of Statistics , National Cheng Kung University , Tainan 701 , Taiwan
| | - Yu-Yi Pan
- Department of Statistics , National Cheng Kung University , Tainan 701 , Taiwan
| | - Chia-Lung Shih
- Department of Environmental and Occupational Health, College of Medicine , National Cheng Kung University , Tainan 701 , Taiwan
| | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry , Moscow 119121 , Russia
| | - Chin-Shang Li
- School of Nursing , The State University of New York, University at Buffalo , Buffalo , New York 14214 , United States
| | | | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine , National Cheng Kung University , Tainan 701 , Taiwan
| |
Collapse
|
16
|
Seale B, Schneider BB, Le Blanc JCY. Enhancing signal and mitigating up-front peptide fragmentation using controlled clustering by gas-phase modifiers. Anal Bioanal Chem 2019; 411:6365-6376. [DOI: 10.1007/s00216-019-02036-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 01/11/2023]
|
17
|
Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
Collapse
Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
18
|
A practical approach to enrich intact tryptic N-glycopeptides through size exclusion chromatography and hydrophilicity (SELIC) using an acrylamide-agarose composite gel system. Anal Chim Acta 2019; 1058:107-116. [PMID: 30851844 DOI: 10.1016/j.aca.2019.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 12/18/2022]
Abstract
Increasing researches proved that abnormal glycosylation is strongly correlated with many diseases. Specially, site-specific glycosylation and its associated heterogeneity are closely related to the function and activity of the glycoprotein. However, intact N-glycopeptide analysis still faces great challenges because the presence of highly abundant non-glycosylated peptides would suppress the ionization of lowly abundant glycopeptides. In the present study, we developed a practical intact tryptic N-glycopeptide enrichment method using acrylamide-agarose composite gel that combined the size exclusion chromatography and hydrophilic (named SELIC) effects, aimed to remove the detergent rapidly and effectively, as well as enrich intact N-glycopeptides while extracting peptides. This is a useful tool to facilitate the intact N-glycopeptides analysis of complex protein mixtures, particularly for samples that extracted from formalin-fixed and paraffin-embedded (FFPE) tissues by SDS. Using this method, we successfully identified 700 site-specific intact tryptic N-glycopeptides corresponding to 261 glycosylation sites on 191 glycoproteins from FFPE thymoma tissues.
Collapse
|
19
|
Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
Collapse
Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| |
Collapse
|
20
|
Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. Quality control in mass spectrometry-based proteomics. MASS SPECTROMETRY REVIEWS 2018; 37:697-711. [PMID: 28802010 DOI: 10.1002/mas.21544] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 05/21/2023]
Abstract
Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results. A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages. We review potential sources of variability that can impact the results of a mass spectrometry experiment occurring in all of these steps, and we discuss how to monitor and remedy the negative influences on the experimental results. Furthermore, we describe how specialized quality control samples of varying sample complexity can be incorporated into the experimental workflow and how they can be used to rigorously assess detailed aspects of the instrument performance.
Collapse
Affiliation(s)
- Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg Hospital, Cape Town, South Africa
| | - Francis Impens
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| |
Collapse
|
21
|
Abstract
Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.
Collapse
Affiliation(s)
- Isidro Ferrer
- Pathologic Anatomy Service, Institute of Neuropathology, Bellvitge University Hospital; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona; and Network Center of Biomedical Research on Neurodegenerative Diseases, Institute Carlos III; Hospitalet de Llobregat, Llobregat, Spain.
| |
Collapse
|
22
|
Nigam A, Subramanian M, Koiram Rajanna P. Non-specific Digestion Artifacts of Bovine Trypsin Exemplified with Surrogate Peptides for Endogenous Protein Quantitation. Chromatographia 2017. [DOI: 10.1007/s10337-017-3424-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
23
|
Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics 2016; 15:1773-90. [PMID: 26929216 PMCID: PMC5083109 DOI: 10.1074/mcp.o115.057638] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.
Collapse
Affiliation(s)
- Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia;
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Schulz
- §School of Chemistry & Molecular Biosciences, St Lucia, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
24
|
Trevisiol S, Ayoub D, Lesur A, Ancheva L, Gallien S, Domon B. The use of proteases complementary to trypsin to probe isoforms and modifications. Proteomics 2016; 16:715-28. [DOI: 10.1002/pmic.201500379] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/06/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Stéphane Trevisiol
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Daniel Ayoub
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Antoine Lesur
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Lina Ancheva
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Sébastien Gallien
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| |
Collapse
|
25
|
Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI, Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. Anal Chem 2015; 88:95-121. [PMID: 26558748 DOI: 10.1021/acs.analchem.5b04230] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Xu Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Amanda E Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Shelley Deeke
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Bo Xu
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Ming Wen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Kai Cheng
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Deeptee Seebun
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Alexandra Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| |
Collapse
|