1
|
Song JG, Baral KC, Kim GL, Park JW, Seo SH, Kim DH, Jung DH, Ifekpolugo NL, Han HK. Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques. Drug Deliv 2023; 30:2183816. [PMID: 36880122 PMCID: PMC10003146 DOI: 10.1080/10717544.2023.2183816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.
Collapse
Affiliation(s)
- Jae Geun Song
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Kshitis Chandra Baral
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Gyu-Lin Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Ji-Won Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Soo-Hwa Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Da-Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Dong Hoon Jung
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Nonye Linda Ifekpolugo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Hyo-Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| |
Collapse
|
2
|
Battellino T, Ogata K, Spicer V, Ishihama Y, Krokhin O. Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid. J Proteome Res 2023; 22:272-278. [PMID: 36480176 DOI: 10.1021/acs.jproteome.2c00388] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the general acceptance of formic acid as the additive of choice for peptide reversed-phase LC-MS/MS applications, some still argue that the selection of acetic acid represents a better option. To settle this debate, we investigated both the difference in MS sensitivity and chromatographic behavior of peptides between these two systems. This interlaboratory study was performed using different MS setups and C18 separation media employing both 0.1% formic and 0.5% acetic acid as ion pairing modifiers. Relative to formic acid, we find an overall ∼2.2-2.5× increase in MS signal and a slight decrease in RP LC retention (-0.7% acetonitrile on average) for acetic acid conditions. While these two features have opposing effects on peptide detectability, we find that acetic acid produces up to 60% higher peptide ID output depending on the type of sample. The drop in RPLC retention increases with peptide net charge at acidic pH. MS signal is dependent on the difference between the charge of the precursor ion and the charge of the peptide in solution, favoring species with a low pI. Lower peptide retention under acetic acid conditions demonstrates its higher hydrophilicity and, as expected, leads to composition and sequence-dependent character of the observed retention shift.
Collapse
Affiliation(s)
- Taylor Battellino
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Oleg Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada.,University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| |
Collapse
|
3
|
V G, Basuri PP, Sahini K, C N N. Retention behaviour of analytes in reversed phase high performance liquid chromatography - A review. Biomed Chromatogr 2022:e5482. [PMID: 35962484 DOI: 10.1002/bmc.5482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022]
Abstract
The understanding of principles that drive the separation in reversed phase chromatography plays an important role in the prediction of elution of solutes in RP-HPLC. The separation in RP-HPLC is based on the principle of adsorption and partition. In addition, the log P value, pKa value of the drug, chromatographic parameters like mobile phase pH, buffer concentration, organic modifier and mobile phase additives also influence the retention and selectivity of the analyte. It is found that hydrophobic, electrostatic, hydrogen bonding and other specific interactions between the stationary phase and the solutes along with the hydrophobicity of an analyte molecule (log P) modify the retention behaviour of the analytes. This article gives special attention to the influence of ionization and ion interaction on the separation of analytes. The drug molecules with different log P value containing protonated and deprotonated acids, bases and zwitterions are selected as examples and this article addresses various issues related to method development, relationships between analyte retention and mobile phase pH and pKa value of the analyte. The advances in this regard, with highlights on topics such as mechanisms of retention and various factors that influence the retention behaviour of analytes is also updated with suitable examples.
Collapse
Affiliation(s)
- Ganesh V
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| | - P Poorna Basuri
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| | - K Sahini
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| | - Nalini C N
- Department of Pharmaceutical analysis, C. L. Baid Metha College of pharmacy, Chennai, India
| |
Collapse
|
4
|
Khalaf R, Baur D, Pfister D. Optimization of reversed-phase chromatography methods for peptide analytics. J Chromatogr A 2015; 1425:198-203. [DOI: 10.1016/j.chroma.2015.11.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/30/2022]
|
5
|
Biller J, Morschheuser L, Riedner M, Rohn S. Development of optimized mobile phases for protein separation by high performance thin layer chromatography. J Chromatogr A 2015; 1415:146-54. [PMID: 26341592 DOI: 10.1016/j.chroma.2015.08.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 01/12/2023]
Abstract
In recent years, protein chemistry tends inexorably toward the analysis of more complex proteins, proteoforms, and posttranslational protein modifications. Although mass spectrometry developed quite fast correspondingly, sample preparation and separation of these analytes is still a major issue and quite challenging. For many years, electrophoresis seemed to be the method of choice; nonetheless its variance is limited to parameters such as size and charge. When taking a look at traditional (thin-layer) chromatography, further parameters such as polarity and different mobile and stationary phases can be utilized. Further, possibilities of detection are manifold compared to electrophoresis. Similarly, two-dimensional separation can be also performed with thin-layer chromatography (TLC). As the revival of TLC developed enormously in the last decade, it seems to be also an alternative to use high performance thin-layer chromatography (HPTLC) for the separation of proteins. The aim of this study was to establish an HPTLC separation system that allows a separation of protein mixtures over a broad polarity range, or if necessary allowing to modify the separation with only few steps to improve the separation for a specific scope. Several layers and solvent systems have been evaluated to reach a fully utilized and optimized separation system.
Collapse
Affiliation(s)
- Julia Biller
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Lena Morschheuser
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Maria Riedner
- Institute of Organic Chemistry, Mass Spectrometric Facility, University of Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - Sascha Rohn
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany.
| |
Collapse
|
6
|
Influence of sample and mobile phase composition on peptide retention behaviour and sensitivity in reversed-phase liquid chromatography/mass spectrometry. J Chromatogr A 2013; 1314:199-207. [DOI: 10.1016/j.chroma.2013.09.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/20/2022]
|
7
|
Odunuga OO, Shazhko A. Ammonium sulfate precipitation combined with liquid chromatography is sufficient for purification of bovine serum albumin that is suitable for most routine laboratory applications. ACTA ACUST UNITED AC 2013. [DOI: 10.7243/2052-9341-1-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
8
|
Houbart V, Cobraiville G, Lecomte F, Debrus B, Hubert P, Fillet M. Development of a nano-liquid chromatography on chip tandem mass spectrometry method for high-sensitivity hepcidin quantitation. J Chromatogr A 2011; 1218:9046-54. [PMID: 22055522 DOI: 10.1016/j.chroma.2011.10.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
Abstract
Microfluidic LC systems present undeniable advantages over classical LC in terms of sensitivity. Hepcidin, a peptide marker of clinical disorders linked to iron metabolism, was used as model to demonstrate peptide quantification potentialities of LC-chip coupled to a nanoelectrospray source ion trap mass spectrometer in an aqueous sample. First, stable isotope labelled hepcidin was chosen as internal standard and gradient as well as sample compositions were optimised using design of experiments as development tool. The method was then prevalidated using accuracy profiles in order to select the most appropriate response function and to confirm the ability of the technique to quantify low hepcidin concentration. A reliable and very sensitive quantitation method was finally obtained using this integrated microfluidic technology. Indeed, good results with respect to accuracy, trueness and precision were achieved, as well as a very low limit of quantitation (0.07 ng/ml). Method suitability of nano-LC on chip tandem mass spectrometry for hepcidin quantitation was also demonstrated in complex media such as human plasma.
Collapse
Affiliation(s)
- V Houbart
- Laboratory of Analytical Pharmaceutical Chemistry, Department of Pharmacy, CIRM, University of Liège, Belgium
| | | | | | | | | | | |
Collapse
|
9
|
Wang NH, Lee WL, Her GR. Signal Enhancement for Peptide Analysis in Liquid Chromatography–Electrospray Ionization Mass Spectrometry with Trifluoroacetic Acid Containing Mobile Phase by Postcolumn Electrophoretic Mobility Control. Anal Chem 2011; 83:6163-8. [DOI: 10.1021/ac2003714] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nan-Hsuan Wang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Wan-Li Lee
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Guor-Rong Her
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
10
|
Jandera P, Krupczyńska K, Vyňuchalová K, Buszewski B. Combined effects of mobile phase composition and temperature on the retention of homologous and polar test compounds on polydentate C8 column. J Chromatogr A 2010; 1217:6052-60. [DOI: 10.1016/j.chroma.2010.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/01/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
|
11
|
Peterson A, Hohmann L, Huang L, Kim B, Eng JK, Martin DB. Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics. J Proteome Res 2009; 8:4161-8. [PMID: 19601632 DOI: 10.1021/pr9001417] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substantial energy and resources have been invested in improving mass spectrometry (MS) instrumentation, upstream sample preparation protocols, and database search strategies to maximize peptide and protein identifications. The role of HPLC sample loading methods in maximizing MS identifications has been largely overlooked, and there exists an immense heterogeneity in the methods employed in the proteomics literature. We sought to optimize loading methods by testing multiple loading conditions (buffer composition, resin, initial gradient) using tryptic digests of an 18 protein mixture and whole yeast lysate. The loading buffer acetonitrile (ACN) concentration greatly affected peptide identifications: up to a 26% increase in peptide identifications was observed by decreasing the ACN concentration from 5 to 2% during sample loading. Hydrophilic peptides were the main contributors to the increase in peptide identifications and, at higher ACN concentrations, were washed from the precolumn during desalting. Sampling of the hydrophilic peptides was enhanced by using a shallow initial ACN gradient. The results were found to be resin-specific and not generalizable. Our investigation demonstrates the often unappreciated importance of optimizing sample loading conditions to reflect the aims of the research and the characteristics of the LC configurations employed.
Collapse
Affiliation(s)
- Amelia Peterson
- Department of Chemistry, University of Wisconsin, Madison, USA
| | | | | | | | | | | |
Collapse
|
12
|
Burgess KEV, Lainson A, Imrie L, Fraser-Pitt D, Yaga R, Smith DGE, Swart R, Pitt AR, Inglis NF. Performance of five different electrospray ionisation sources in conjunction with rapid monolithic column liquid chromatography and fast MS/MS scanning. Proteomics 2009; 9:1720-6. [PMID: 19242933 DOI: 10.1002/pmic.200800200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performances of five different ESI sources coupled to a polystyrene-divinylbenzene monolithic column were compared in a series of LC-ESI-MS/MS analyses of Escherichia coli outer membrane proteins. The sources selected for comparison included two different modifications of the standard electrospray source, a commercial low-flow sprayer, a stainless steel nanospray needle and a coated glass Picotip. Respective performances were judged on sensitivity and the number and reproducibility of significant protein identifications obtained through the analysis of multiple identical samples. Data quality varied between that of a ground silica capillary, with 160 total protein identifications, the lowest number of high quality peptide hits obtained (3012), and generally peaks of lower intensity; and a stainless steel nanospray needle, which resulted in increased precursor ion abundance, the highest-quality peptide fragmentation spectra (5414) and greatest number of total protein identifications (259) exhibiting the highest MASCOT scores (average increase in score of 27.5% per identified protein). The data presented show that, despite increased variability in comparative ion intensity, the stainless steel nanospray needle provides the highest overall sensitivity. However, the resulting data were less reproducible in terms of proteins identified in complex mixtures -- arguably due to an increased number of high intensity precursor ion candidates.
Collapse
Affiliation(s)
- Karl E V Burgess
- Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Poole CF, Poole SK. Foundations of retention in partition chromatography. J Chromatogr A 2009; 1216:1530-50. [PMID: 19013576 DOI: 10.1016/j.chroma.2008.10.092] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 10/22/2008] [Accepted: 10/28/2008] [Indexed: 10/21/2022]
|
14
|
|
15
|
Jandera P, Novotná K. Characterization of High‐Pressure Liquid Chromatography Columns using Chromatographic Methods. ANAL LETT 2006. [DOI: 10.1080/00032710600773424] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
16
|
McCalley DV. Effect of buffer on peak shape of peptides in reversed-phase high performance liquid chromatography. J Chromatogr A 2004; 1038:77-84. [PMID: 15233523 DOI: 10.1016/j.chroma.2004.03.038] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The effect of changing the buffer at constant low pH in the mobile phase is investigated with respect to the separation of a mixture of basic peptides. Considerably worse peak shapes, leading to poorer resolution of complex peptide mixtures, were obtained when using formic acid favoured in LC-MS applications compared with non volatile phosphate buffers or with trifluoroacetic acid (TFA). Poorer peak shapes were largely attributable to reduced column capacity for the peptides when using mobile phases of low ionic strength, due to the increased mutual repulsion of ions held on the hydrophobic column surface which is facilitated in these buffers. However, ion-pairing between the peptides and additives such as TFA or even phosphate may also lessen mutual repulsion effects, leading to greater column capacity. Overloading effects could be observed when sample masses around only 0.1 microg were injected on to standard size analytical columns in formic acid containing mobile phases; sample masses around only 1.5 microg may cause loss of half the system peak capacity in such mobile phases. Results were broadly comparable (after scaling sample size according to column diameter) on columns of both conventional (4.6 mm i.d.) and capillary (0.075 mm i.d.) dimensions. Ammonium formate may be a useful alternative buffer for some applications due to its higher ionic strength.
Collapse
Affiliation(s)
- David V McCalley
- Faculty of Applied Sciences, Centre for Research in Biomedicine, Frenchay Campus, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK.
| |
Collapse
|