1
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Li X, Pierson NA, Hua X, Patel BA, Olma MH, Strulson CA, Letarte S, Richardson DD. Analytical Performance Evaluation of Identity, Quality-Attribute Monitoring and new Peak Detection in a Platform Multi-Attribute Method Using Lys-C Digestion for Characterization and Quality Control of Therapeutic Monoclonal Antibodies. J Pharm Sci 2023; 112:691-699. [PMID: 36279953 DOI: 10.1016/j.xphs.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
Abstract
The use of multi-attribute method (MAM) for identity and purity testing of biopharmaceuticals offers the ability to complement and replace multiple conventional analytical technologies with a single mass spectrometry (MS) method. Phase-appropriate method validation is one major consideration for the implementation of MAM in a current Good Manufacturing Practice (cGMP) environment. We developed a MAM workflow for therapeutic monoclonal antibodies (mAbs) with optimized sample preparation using lysyl endopeptidase (Lys-C) digestion. In this study, we evaluated the assay performances of this platform MAM workflow for identity, product quality attributes (PQAs) monitoring and new peak detection (NPD) for single and coformulated mAbs. An IgG4 mAb-1 and its coformulations were used as model molecules in this study. The assay performance evaluation demonstrated the full potential of the platform MAM approach for its intended use for characterization and quality control of single mAb-1 and mAb-1 in its coformulations. To the best of our knowledge, this is the first performance evaluation of MAM for mAb identity, PQA monitoring, and new peak detection (NPD) in a single assay, featuring 1) the first performance evaluation of MAM for PQA monitoring using Lys-C digestion with a high-resolution MS, 2) a new approach for mAb identity testing capable of distinguishing single mAb from coformulations using MAM, and 3) the performance evaluation of NPD for MAM with Lys-C digestion. The developed platform MAM workflow and the MAM performance evaluation paved the way for its GMP qualification and enabled clinical release of mAb-1 in GMP environment with MAM.
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Affiliation(s)
- Xuanwen Li
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States.
| | - Nicholas A Pierson
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Xiaoqing Hua
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Bhumit A Patel
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Michael H Olma
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Christopher A Strulson
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Simon Letarte
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Douglas D Richardson
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
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2
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Mouchahoir T, Schiel JE, Rogers R, Heckert A, Place BJ, Ammerman A, Li X, Robinson T, Schmidt B, Chumsae CM, Li X, Manuilov AV, Yan B, Staples GO, Ren D, Veach AJ, Wang D, Yared W, Sosic Z, Wang Y, Zang L, Leone AM, Liu P, Ludwig R, Tao L, Wu W, Cansizoglu A, Hanneman A, Adams GW, Perdivara I, Walker H, Wilson M, Brandenburg A, DeGraan-Weber N, Gotta S, Shambaugh J, Alvarez M, Yu XC, Cao L, Shao C, Mahan A, Nanda H, Nields K, Nightlinger N, Niu B, Wang J, Xu W, Leo G, Sepe N, Liu YH, Patel BA, Richardson D, Wang Y, Tizabi D, Borisov OV, Lu Y, Maynard EL, Gruhler A, Haselmann KF, Krogh TN, Sönksen CP, Letarte S, Shen S, Boggio K, Johnson K, Ni W, Patel H, Ripley D, Rouse JC, Zhang Y, Daniels C, Dawdy A, Friese O, Powers TW, Sperry JB, Woods J, Carlson E, Sen KI, Skilton SJ, Busch M, Lund A, Stapels M, Guo X, Heidelberger S, Kaluarachchi H, McCarthy S, Kim J, Zhen J, Zhou Y, Rogstad S, Wang X, Fang J, Chen W, Yu YQ, Hoogerheide JG, Scott R, Yuan H. Attribute Analytics Performance Metrics from the MAM Consortium Interlaboratory Study. J Am Soc Mass Spectrom 2022; 33:1659-1677. [PMID: 36018776 PMCID: PMC9460773 DOI: 10.1021/jasms.2c00129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 05/23/2023]
Abstract
The multi-attribute method (MAM) was conceived as a single assay to potentially replace multiple single-attribute assays that have long been used in process development and quality control (QC) for protein therapeutics. MAM is rooted in traditional peptide mapping methods; it leverages mass spectrometry (MS) detection for confident identification and quantitation of many types of protein attributes that may be targeted for monitoring. While MAM has been widely explored across the industry, it has yet to gain a strong foothold within QC laboratories as a replacement method for established orthogonal platforms. Members of the MAM consortium recently undertook an interlaboratory study to evaluate the industry-wide status of MAM. Here we present the results of this study as they pertain to the targeted attribute analytics component of MAM, including investigation into the sources of variability between laboratories and comparison of MAM data to orthogonal methods. These results are made available with an eye toward aiding the community in further optimizing the method to enable its more frequent use in the QC environment.
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Affiliation(s)
- Trina Mouchahoir
- National
Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, Maryland 20850, United States
| | - John E. Schiel
- National
Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, Maryland 20850, United States
| | - Rich Rogers
- Just-Evotech
Biologics, Inc., 401
Terry Ave N., Seattle, Washington 98109, United States
| | - Alan Heckert
- National
Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
| | - Benjamin J. Place
- National
Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
| | - Aaron Ammerman
- AbbVie, 1000 Gateway
Blvd, South San Francisco, California 94080, United States
| | - Xiaoxiao Li
- AbbVie, 1000 Gateway
Blvd, South San Francisco, California 94080, United States
| | - Tom Robinson
- AbbVie, 1000 Gateway
Blvd, South San Francisco, California 94080, United States
| | - Brian Schmidt
- AbbVie, 1000 Gateway
Blvd, South San Francisco, California 94080, United States
| | - Chris M. Chumsae
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Xinbi Li
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Anton V. Manuilov
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Bo Yan
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Gregory O. Staples
- Agilent
Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 95008, United States
| | - Da Ren
- Amgen, One Amgen Center Dr, Thousand
Oaks, California 91320, United States
| | - Alexander J. Veach
- Amgen, One Amgen Center Dr, Thousand
Oaks, California 91320, United States
| | - Dongdong Wang
- BioAnalytix, 790 Memorial Dr, Cambridge, Massachusetts 02139, United States
| | - Wael Yared
- BioAnalytix, 790 Memorial Dr, Cambridge, Massachusetts 02139, United States
| | - Zoran Sosic
- Biogen, 125 Broadway, Cambridge, Massachusetts 02142, United States
| | - Yan Wang
- Biogen, 125 Broadway, Cambridge, Massachusetts 02142, United States
| | - Li Zang
- Biogen, 125 Broadway, Cambridge, Massachusetts 02142, United States
| | - Anthony M. Leone
- Bristol-Myers
Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Peiran Liu
- Bristol-Myers
Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Richard Ludwig
- Bristol-Myers
Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Li Tao
- Bristol-Myers
Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Wei Wu
- Bristol-Myers
Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Ahmet Cansizoglu
- Charles
River Laboratories, 8
Henshaw Street, Shrewsbury, Massachusetts 01801, United States
| | - Andrew Hanneman
- Charles
River Laboratories, 8
Henshaw Street, Shrewsbury, Massachusetts 01801, United States
| | - Greg W. Adams
- FUJIFILM
Diosynth Biotechnologies, 101 J. Morris Commons Ln, Morrisville, North Carolina 27560, United States
| | - Irina Perdivara
- FUJIFILM
Diosynth Biotechnologies, 101 J. Morris Commons Ln, Morrisville, North Carolina 27560, United States
| | - Hunter Walker
- FUJIFILM
Diosynth Biotechnologies, 101 J. Morris Commons Ln, Morrisville, North Carolina 27560, United States
| | - Margo Wilson
- FUJIFILM
Diosynth Biotechnologies, 101 J. Morris Commons Ln, Morrisville, North Carolina 27560, United States
| | | | - Nick DeGraan-Weber
- Genedata, 750 Marrett Road, One Cranberry
Hill, Lexington, Massachusetts 02421, United States
| | - Stefano Gotta
- Genedata, Margarethenstrasse 38, Basel, 4053, Switzerland
| | - Joe Shambaugh
- Genedata, 750 Marrett Road, One Cranberry
Hill, Lexington, Massachusetts 02421, United States
| | - Melissa Alvarez
- Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - X. Christopher Yu
- Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Li Cao
- GSK, 709
Swedeland Rd, King of Prussia, Pennsylvania 19406, United States
| | - Chun Shao
- GSK, 709
Swedeland Rd, King of Prussia, Pennsylvania 19406, United States
| | - Andrew Mahan
- Janssen, 1400 McKean Road, Springhouse, Pennsylvania 19477, United States
| | - Hirsh Nanda
- Janssen, 1400 McKean Road, Springhouse, Pennsylvania 19477, United States
| | - Kristen Nields
- Janssen, 1400 McKean Road, Springhouse, Pennsylvania 19477, United States
| | - Nancy Nightlinger
- Just-Evotech
Biologics, Inc., 401
Terry Ave N., Seattle, Washington 98109, United States
| | - Ben Niu
- AstraZeneca, One MedImmune Way, Gaithersburg, Maryland 20878, United
States
| | - Jihong Wang
- AstraZeneca, One MedImmune Way, Gaithersburg, Maryland 20878, United
States
| | - Wei Xu
- AstraZeneca, One MedImmune Way, Gaithersburg, Maryland 20878, United
States
| | - Gabriella Leo
- EMD Serono an affiliate of Merck KGaA, Darmstadt, Germany, Via Luigi Einaudi 11, Guidonia Montecelio (Roma), 00012, Italy
| | - Nunzio Sepe
- EMD Serono an affiliate of Merck KGaA, Darmstadt, Germany, Via Luigi Einaudi 11, Guidonia Montecelio (Roma), 00012, Italy
| | - Yan-Hui Liu
- Merck
& Co., Inc.., 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Bhumit A. Patel
- Merck
& Co., Inc.., 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Douglas Richardson
- Merck
& Co., Inc.., 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Yi Wang
- Merck
& Co., Inc.., 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Daniela Tizabi
- National
Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, Maryland 20850, United States
| | - Oleg V. Borisov
- Novavax,
Inc., 20 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Yali Lu
- Novavax,
Inc., 20 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Ernest L. Maynard
- Novavax,
Inc., 20 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | | | | | | | | | - Simon Letarte
- Pfizer, 375 N Field Dr, Lake Forest, Illinois 60045, United
States
| | - Sean Shen
- Pfizer, 375 N Field Dr, Lake Forest, Illinois 60045, United
States
| | - Kristin Boggio
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - Keith Johnson
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - Wenqin Ni
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - Himakshi Patel
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - David Ripley
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - Jason C. Rouse
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - Ying Zhang
- Pfizer, 1 Burtt Rd, Andover, Massachusetts 01810, United States
| | - Carly Daniels
- Pfizer, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Andrew Dawdy
- Pfizer, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Olga Friese
- Pfizer, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Thomas W. Powers
- Pfizer, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Justin B. Sperry
- Pfizer, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Josh Woods
- Pfizer, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Eric Carlson
- Protein
Metrics, Inc., 20863
Stevens Creek Blvd, Cupertino, California 95014, United States
| | - K. Ilker Sen
- Protein
Metrics, Inc., 20863
Stevens Creek Blvd, Cupertino, California 95014, United States
| | - St John Skilton
- Protein
Metrics, Inc., 20863
Stevens Creek Blvd, Cupertino, California 95014, United States
| | - Michelle Busch
- Sanofi, 1 The Mountain Rd, Framingham, Massachusetts 01701, United States
| | - Anders Lund
- Sanofi, 1 The Mountain Rd, Framingham, Massachusetts 01701, United States
| | - Martha Stapels
- Sanofi, 1 The Mountain Rd, Framingham, Massachusetts 01701, United States
| | - Xu Guo
- SCIEX, 71 Four Valley Drive, Concord, ON L4K
4V8, Canada
| | | | | | - Sean McCarthy
- SCIEX, 500 Old Connecticut Path, Framingham, Massachusetts 01701, United States
| | - John Kim
- Teva, 145 Brandywine Pkwy, West Chester, Pennsylvania 19380, United States
| | - Jing Zhen
- Teva, 145 Brandywine Pkwy, West Chester, Pennsylvania 19380, United States
| | - Ying Zhou
- Teva, 145 Brandywine Pkwy, West Chester, Pennsylvania 19380, United States
| | - Sarah Rogstad
- U.S. Food
and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland 20993, United States
| | - Xiaoshi Wang
- U.S. Food
and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland 20993, United States
| | - Jing Fang
- Waters, 34 Maple St, Milford, Massachusetts 01757, United States
| | - Weibin Chen
- Waters, 34 Maple St, Milford, Massachusetts 01757, United States
| | - Ying Qing Yu
- Waters, 34 Maple St, Milford, Massachusetts 01757, United States
| | | | - Rebecca Scott
- Zoetis, 333 Portage St, Kalamazoo, Michigan 49007, United
States
| | - Hua Yuan
- Zoetis, 333 Portage St, Kalamazoo, Michigan 49007, United
States
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3
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Li X, Rawal B, Rivera S, Letarte S, Richardson DD. Improvements on sample preparation and peptide separation for reduced peptide mapping based multi-attribute method analysis of therapeutic monoclonal antibodies using lysyl endopeptidase digestion. J Chromatogr A 2022; 1675:463161. [DOI: 10.1016/j.chroma.2022.463161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/14/2022]
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4
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Yang RS, Bush DR, DeGraan-Weber N, Barbacci D, Zhang LK, Letarte S, Richardson D. Advancing Structure Characterization of PS-80 by Charge-Reduced Mass Spectrometry and Software-Assisted Composition Analysis. J Pharm Sci 2021; 111:314-322. [PMID: 34487745 DOI: 10.1016/j.xphs.2021.08.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
The commercially available Polysorbate 80 (PS-80) is a highly heterogeneous product. It is a complex and structurally diverse mixture consisting of polymeric species containing polyoxyethylenes (POEs), fatty acid esters, with/or without a carbohydrate core. The core is primarily sorbitan, with some isosorbide and sorbitol. Depending on the sources of fatty acids and the degrees of esterification, multiple combinations of fatty acid esters are commonly observed. A number of POE intermediates, such as polyoxyethylene glycols, POE-sorbitans, POE-isosorbides, and an array of fatty acid esters from these intermediates remain in the raw material as well. The complex composition of PS-80 is difficult to control and poses a significant characterization challenge for its use in the pharmaceutical industry. Here, we present a novel solution for PS-80 characterization using ultra high-performance liquid chromatography coupled with charge-reduction high resolution mass spectrometry. Post column co-infusion of triethylamine focused the signal into mainly singly charged molecular ions and reduced the extent of in-source fragmentation, resulting in a simpler ion map and enhanced measurement of PS-80 species. The data processing workflow is designed to programmatically identify PS-80 component classes and reduce the burden of manually analyzing complex MS data. The 2-dimensional graphical representation of the data helps visualize these features. Together, these innovative methodologies enabled us to analyze components in PS-80 with unprecedented detail and shall be a useful tool to study formulation and stability of pharmaceutical preparations. The power of this approach was demonstrated by comparing the composition of PS-80 obtained from different vendors.
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Affiliation(s)
- Rong-Sheng Yang
- Analytical Research & Development, Merck & Co., Inc, Kenilworth, New Jersey 07033, United States.
| | | | | | - Damon Barbacci
- Analytical Research & Development, Merck & Co., Inc, Kenilworth, New Jersey 07033, United States
| | - Li-Kang Zhang
- Analytical Research & Development, Merck & Co., Inc, Kenilworth, New Jersey 07033, United States
| | - Simon Letarte
- Analytical Research & Development, Merck & Co., Inc, Kenilworth, New Jersey 07033, United States
| | - Douglas Richardson
- Analytical Research & Development, Merck & Co., Inc, Kenilworth, New Jersey 07033, United States
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5
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Li X, Chandra D, Letarte S, Adam GC, Welch J, Yang RS, Rivera S, Bodea S, Dow A, Chi A, Strulson CA, Richardson DD. Profiling Active Enzymes for Polysorbate Degradation in Biotherapeutics by Activity-Based Protein Profiling. Anal Chem 2021; 93:8161-8169. [PMID: 34032423 DOI: 10.1021/acs.analchem.1c00042] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Polysorbate is widely used to maintain stability of biotherapeutic proteins in pharmaceutical formulation development. Degradation of polysorbate can lead to particle formation in drug products, which is a major quality concern and potential patient risk factor. Enzymatic activity from residual host cell enzymes such as lipases and esterases plays a major role for polysorbate degradation. Their high activity, often at very low concentration, constitutes a major analytical challenge in the biopharmaceutical industry. In this study, we evaluated and optimized the activity-based protein profiling (ABPP) approach to identify active enzymes responsible for polysorbate degradation. Using an optimized chemical probe, we established the first global profile of active serine hydrolases in harvested cell culture fluid (HCCF) for monoclonal antibodies (mAbs) production from two Chinese hamster ovary (CHO) cell lines. A total of eight known lipases were identified by ABPP with enzyme activity information, while only five lipases were identified by a traditional abundance-based proteomics (TABP) approach. Interestingly, phospholipase B-like 2 (PLBL2), a well-known problematic HCP was not found to be active in process-intermediates from two different mAbs. In a proof-of-concept study with downstream samples, phospholipase A2 group VII (PLA2G7) was only identified by ABPP and confirmed to contribute to polysorbate-80 degradation for the first time. The established ABBP approach is approved to be able to identify low-abundance host cell enzymes and fills the gap between lipase abundance and activity, which enables more meaningful polysorbate degradation investigations for biotherapeutic development.
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Affiliation(s)
- Xuanwen Li
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Divya Chandra
- Biologics Process Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Simon Letarte
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Gregory C Adam
- Quantitative Biosciences, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Jonathan Welch
- Biologics Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Rong-Sheng Yang
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Shannon Rivera
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Smaranda Bodea
- Chemical Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Alex Dow
- Biologics Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - An Chi
- Chemical Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Christopher A Strulson
- Biologics Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Douglas D Richardson
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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6
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Mouchahoir T, Schiel JE, Rogers R, Heckert A, Place BJ, Ammerman A, Li X, Robinson T, Schmidt B, Chumsae CM, Li X, Manuilov AV, Yan B, Staples GO, Ren D, Veach AJ, Wang D, Yared W, Sosic Z, Wang Y, Zang L, Leone AM, Liu P, Ludwig R, Tao L, Wu W, Cansizoglu A, Hanneman A, Adams GW, Perdivara I, Walker H, Wilson M, Brandenburg A, DeGraan-Weber N, Gotta S, Shambaugh J, Alvarez M, Yu XC, Cao L, Shao C, Mahan A, Nanda H, Nields K, Nightlinger N, Barysz HM, Jahn M, Niu B, Wang J, Leo G, Sepe N, Liu YH, Patel BA, Richardson D, Wang Y, Tizabi D, Borisov OV, Lu Y, Maynard EL, Gruhler A, Haselmann KF, Krogh TN, Sönksen CP, Letarte S, Shen S, Boggio K, Johnson K, Ni W, Patel H, Ripley D, Rouse JC, Zhang Y, Daniels C, Dawdy A, Friese O, Powers TW, Sperry JB, Woods J, Carlson E, Sen KI, Skilton SJ, Busch M, Lund A, Stapels M, Guo X, Heidelberger S, Kaluarachchi H, McCarthy S, Kim J, Zhen J, Zhou Y, Rogstad S, Wang X, Fang J, Chen W, Yu YQ, Hoogerheide JG, Scott R, Yuan H. New Peak Detection Performance Metrics from the MAM Consortium Interlaboratory Study. J Am Soc Mass Spectrom 2021; 32:913-928. [PMID: 33710905 DOI: 10.1021/jasms.0c00415] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The Multi-Attribute Method (MAM) Consortium was initially formed as a venue to harmonize best practices, share experiences, and generate innovative methodologies to facilitate widespread integration of the MAM platform, which is an emerging ultra-high-performance liquid chromatography-mass spectrometry application. Successful implementation of MAM as a purity-indicating assay requires new peak detection (NPD) of potential process- and/or product-related impurities. The NPD interlaboratory study described herein was carried out by the MAM Consortium to report on the industry-wide performance of NPD using predigested samples of the NISTmAb Reference Material 8671. Results from 28 participating laboratories show that the NPD parameters being utilized across the industry are representative of high-resolution MS performance capabilities. Certain elements of NPD, including common sources of variability in the number of new peaks detected, that are critical to the performance of the purity function of MAM were identified in this study and are reported here as a means to further refine the methodology and accelerate adoption into manufacturer-specific protein therapeutic product life cycles.
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Affiliation(s)
- Trina Mouchahoir
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - John E Schiel
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Rich Rogers
- Just - Evotech Biologics, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Alan Heckert
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Benjamin J Place
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Aaron Ammerman
- AbbVie, 1500 Seaport Boulevard, Redwood City, California 94063, United States
| | - Xiaoxiao Li
- AbbVie, 1500 Seaport Boulevard, Redwood City, California 94063, United States
| | - Tom Robinson
- AbbVie, 1500 Seaport Boulevard, Redwood City, California 94063, United States
| | - Brian Schmidt
- AbbVie, 1500 Seaport Boulevard, Redwood City, California 94063, United States
| | - Chris M Chumsae
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Xinbi Li
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Anton V Manuilov
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Bo Yan
- AbbVie, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Gregory O Staples
- Agilent Technologies, 5301 Stevens Creek Boulevard, Santa Clara, California 95008, United States
| | - Da Ren
- Amgen, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Alexander J Veach
- Amgen, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Dongdong Wang
- BioAnalytix, 790 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Wael Yared
- BioAnalytix, 790 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Zoran Sosic
- Biogen, 125 Broadway, Cambridge, Massachusetts 02142, United States
| | - Yan Wang
- Biogen, 125 Broadway, Cambridge, Massachusetts 02142, United States
| | - Li Zang
- Biogen, 125 Broadway, Cambridge, Massachusetts 02142, United States
| | - Anthony M Leone
- Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Peiran Liu
- Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Richard Ludwig
- Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Li Tao
- Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Wei Wu
- Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Ahmet Cansizoglu
- Charles River Laboratories, 8 Henshaw Street, Shrewsbury, Massachusetts 01801, United States
| | - Andrew Hanneman
- Charles River Laboratories, 8 Henshaw Street, Shrewsbury, Massachusetts 01801, United States
| | - Greg W Adams
- FUJIFILM Diosynth Biotechnologies, 101 J. Morris Commons Lane, Morrisville, North Carolina 27560, United States
| | - Irina Perdivara
- FUJIFILM Diosynth Biotechnologies, 101 J. Morris Commons Lane, Morrisville, North Carolina 27560, United States
| | - Hunter Walker
- FUJIFILM Diosynth Biotechnologies, 101 J. Morris Commons Lane, Morrisville, North Carolina 27560, United States
| | - Margo Wilson
- FUJIFILM Diosynth Biotechnologies, 101 J. Morris Commons Lane, Morrisville, North Carolina 27560, United States
| | | | - Nick DeGraan-Weber
- Genedata, 750 Marrett Road, One Cranberry Hill, Lexington, Massachusetts 02421, United States
| | - Stefano Gotta
- Genedata, Margarethenstrasse 38, Basel 4053, Switzerland
| | - Joe Shambaugh
- Genedata, 750 Marrett Road, One Cranberry Hill, Lexington, Massachusetts 02421, United States
| | - Melissa Alvarez
- Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - X Christopher Yu
- Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Li Cao
- GSK, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Chun Shao
- GSK, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Andrew Mahan
- Janssen, 1400 McKean Road, Springhouse, Pennsylvania 19477, United States
| | - Hirsh Nanda
- Janssen, 1400 McKean Road, Springhouse, Pennsylvania 19477, United States
| | - Kristen Nields
- Janssen, 1400 McKean Road, Springhouse, Pennsylvania 19477, United States
| | - Nancy Nightlinger
- Just - Evotech Biologics, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | | | - Michael Jahn
- Lonza, Hochbergerstrasse 60 A, Basel 4057, Switzerland
| | - Ben Niu
- AstraZeneca, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Jihong Wang
- AstraZeneca, One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Gabriella Leo
- EMD Serono, an affiliate of Merck KGaA, Darmstadt, Germany, Via Luigi Einaudi 11, Guidonia Montecelio (Roma) 00012, Italy
| | - Nunzio Sepe
- EMD Serono, an affiliate of Merck KGaA, Darmstadt, Germany, Via Luigi Einaudi 11, Guidonia Montecelio (Roma) 00012, Italy
| | - Yan-Hui Liu
- Merck & Co., Inc., 2000 Galloping Hill Roa, Kenilworth, New Jersey 07033, United States
| | - Bhumit A Patel
- Merck & Co., Inc., 2000 Galloping Hill Roa, Kenilworth, New Jersey 07033, United States
| | - Douglas Richardson
- Merck & Co., Inc., 2000 Galloping Hill Roa, Kenilworth, New Jersey 07033, United States
| | - Yi Wang
- Merck & Co., Inc., 2000 Galloping Hill Roa, Kenilworth, New Jersey 07033, United States
| | - Daniela Tizabi
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Oleg V Borisov
- Novavax, Inc., 20 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Yali Lu
- Novavax, Inc., 20 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Ernest L Maynard
- Novavax, Inc., 20 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | | | | | | | | | - Simon Letarte
- Pfizer, 375 North Field Drive, Lake Forest, Illinois 60045, United States
| | - Sean Shen
- Pfizer, 375 North Field Drive, Lake Forest, Illinois 60045, United States
| | - Kristin Boggio
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Keith Johnson
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Wenqin Ni
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Himakshi Patel
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - David Ripley
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Jason C Rouse
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Ying Zhang
- Pfizer, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Carly Daniels
- Pfizer, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Andrew Dawdy
- Pfizer, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Olga Friese
- Pfizer, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Thomas W Powers
- Pfizer, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Justin B Sperry
- Pfizer, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Josh Woods
- Pfizer, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Eric Carlson
- Protein Metrics, Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - K Ilker Sen
- Protein Metrics, Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - St John Skilton
- Protein Metrics, Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Michelle Busch
- Sanofi, 1 The Mountain Road, Framingham, Massachusetts 01701, United States
| | - Anders Lund
- Sanofi, 1 The Mountain Road, Framingham, Massachusetts 01701, United States
| | - Martha Stapels
- Sanofi, 1 The Mountain Road, Framingham, Massachusetts 01701, United States
| | - Xu Guo
- SCIEX, 71 Four Valley Drive, Concord, ON L4K 4 V8, Canada
| | | | | | - Sean McCarthy
- SCIEX, 500 Old Connecticut Path, Framingham, Massachusetts 01701, United States
| | - John Kim
- Teva, 145 Brandywine Pkwy, West Chester, Pennsylvania 19380, United States
| | - Jing Zhen
- Teva, 145 Brandywine Pkwy, West Chester, Pennsylvania 19380, United States
| | - Ying Zhou
- Teva, 145 Brandywine Pkwy, West Chester, Pennsylvania 19380, United States
| | - Sarah Rogstad
- U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland 20993, United States
| | - Xiaoshi Wang
- U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, Maryland 20993, United States
| | - Jing Fang
- Waters, 34 Maple Street, Milford, Massachusetts 01757, United States
| | - Weibin Chen
- Waters, 34 Maple Street, Milford, Massachusetts 01757, United States
| | - Ying Qing Yu
- Waters, 34 Maple Street, Milford, Massachusetts 01757, United States
| | | | - Rebecca Scott
- Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Hua Yuan
- Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
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7
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Li X, An Y, Liao J, Xiao L, Swanson M, Martinez-Fonts K, Pavon JA, Sherer EC, Jawa V, Wang F, Gao X, Letarte S, Richardson DD. Identification and characterization of a residual host cell protein hexosaminidase B associated with N-glycan degradation during the stability study of a therapeutic recombinant monoclonal antibody product. Biotechnol Prog 2021; 37:e3128. [PMID: 33476097 PMCID: PMC8365702 DOI: 10.1002/btpr.3128] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 12/30/2022]
Abstract
Host cell proteins (HCPs) are process‐related impurities derived from host organisms, which need to be controlled to ensure adequate product quality and safety. In this study, product quality attributes were tracked for several monoclonal antibodies (mAbs) under the intended storage and accelerated stability conditions. One product quality attribute not expected to be stability indicating is the N‐glycan heterogeneity profile. However, significant N‐glycan degradation was observed for one mAb under accelerated and stressed stability conditions. The root cause for this instability was attributed to hexosaminidase B (HEXB), an enzyme known to remove terminal N‐acetylglucosamine (GlcNAc). HEXB was identified by liquid chromatography–mass spectrometry (LC–MS)‐based proteomics approach to be enriched in the impacted stability batches from mAb‐1. Subsequently, enzymatic and targeted multiple reaction monitoring (MRM) MS assays were developed to support process and product characterization. A potential interaction between HEXB and mAb‐1 was initially observed from the analysis of process intermediates by proteomics among several mAbs and later supported by computational modeling. An improved bioprocess was developed to significantly reduce HEXB levels in the final drug substance. A risk assessment was conducted by evaluating the in silico immunogenicity risk and the impact on product quality. To the best of our knowledge, HEXB is the first residual HCP reported to have impact on the glycan profile of a formulated drug product. The combination of different analytical tools, mass spectrometry, and computational modeling provides a general strategy on how to study residual HCP for biotherapeutics development.
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Affiliation(s)
- Xuanwen Li
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Yan An
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jing Liao
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Li Xiao
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Michael Swanson
- Predictive and Clinical Immunogenicity, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Kirby Martinez-Fonts
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jorge Alexander Pavon
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Edward C Sherer
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Vibha Jawa
- Predictive and Clinical Immunogenicity, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Fengqiang Wang
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Xinliu Gao
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Simon Letarte
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Douglas D Richardson
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
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8
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Yang K, Zhang Y, Chou R, Yeung L, Letarte S, Yang RS, Li X, Beaumont M, Gunawan R, Richardson D, Dellatore S, Woolf E, Xu Y. A Tiered Approach for Characterization to Ensure Quality, Reproducibility, and Long-Term Stability of Critical Reagents in Regulated Bioanalysis to Support PK/ADA/NAb Assays for Biologics and Vaccines Programs. ACS Pharmacol Transl Sci 2020; 3:1310-1317. [PMID: 33344904 DOI: 10.1021/acsptsci.0c00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/29/2022]
Abstract
The robustness of good laboratory practice and clinical data is reliant upon a clear understanding of the bioanalytical assays. One of the most important components of ligand-binding based assays is critical reagents used to directly or indirectly measure biologic markers or signals. High quality, reproducible, sustainable critical reagents through the development lifecycle could avoid unnecessary rework, multiple validations, cross-validations, and ensure consistency of the data. Numerous analytical methods (UPLC-size exclusion chromatography, cation exchange chromatography, biacore/octet, and high-resolution mass spectrometry) have been evaluated by using current critical reagents. A comprehensive analytical toolbox of biochemical and biophysical methods has been employed to evaluate the quality of critical reagents and explore potential issues if there are any. Moving forward, this "tiered approach" of critical reagents characterization will be used not only to establish critical quality attributes for new reagents but also to evaluate stability in support of reagents recertification.
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Affiliation(s)
- Kun Yang
- Regulated Bioanalysis, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ying Zhang
- Biologics Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Robert Chou
- Biologics Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lai Yeung
- Regulated Bioanalysis, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Simon Letarte
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Rong-Sheng Yang
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xuanwen Li
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Maribel Beaumont
- Discovery Bioanalysis, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., 213 E Grand Avenue, South San Francisco, California 94080, United States
| | - Rico Gunawan
- Biologics Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Douglas Richardson
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Shara Dellatore
- Regulated Bioanalysis, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Eric Woolf
- Regulated Bioanalysis, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., 770 Sumneytown Pike, WP75B-300, West Point, Pennsylvania 19486, United States
| | - Yang Xu
- Regulated Bioanalysis, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., 770 Sumneytown Pike, WP75B-300, West Point, Pennsylvania 19486, United States
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9
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Sheikh N, Cham J, Zhang L, DeVries T, Letarte S, Pufnock J, Hamm D, Trager J, Fong L. Clonotypic Diversification of Intratumoral T Cells Following Sipuleucel-T Treatment in Prostate Cancer Subjects. Cancer Res 2016; 76:3711-8. [DOI: 10.1158/0008-5472.can-15-3173] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/17/2016] [Indexed: 11/16/2022]
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10
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Fong L, Cham J, Zhang L, DeVries T, Pufnock J, GuhaThakurta D, Letarte S, Hamm D, Trager JB, Sheikh NA. Changes in circulating and intratumoral T cell clonotypes in sipuleucel-T-treated prostate cancer patients. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e16008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Lawrence Fong
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Jason Cham
- Univerisity of California, San Francisco, San Francisco, CA
| | - Li Zhang
- UC San Francisco, San Francisco, CA
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11
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GuhaThakurta D, Sheikh NA, Meagher TC, Letarte S, Trager JB. Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome. Expert Rev Clin Pharmacol 2014; 6:387-401. [DOI: 10.1586/17512433.2013.811814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts JD, Aebersold R. Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Mol Cell Proteomics 2009; 8:1934-46. [PMID: 19411281 DOI: 10.1074/mcp.m800569-mcp200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
As the application for quantitative proteomics in the life sciences has grown in recent years, so has the need for more robust and generally applicable methods for quality control and calibration. The reliability of quantitative proteomics is tightly linked to the reproducibility and stability of the analytical platforms, which are typically multicomponent (e.g. sample preparation, multistep separations, and mass spectrometry) with individual components contributing unequally to the overall system reproducibility. Variations in quantitative accuracy are thus inevitable, and quality control and calibration become essential for the assessment of the quality of the analyses themselves. Toward this end, the use of internal standards cannot only assist in the detection and removal of outlier data acquired by an irreproducible system (quality control) but can also be used for detection of changes in instruments for their subsequent performance and calibration. Here we introduce a set of halogenated peptides as internal standards. The peptides are custom designed to have properties suitable for various quality control assessments, data calibration, and normalization processes. The unique isotope distribution of halogenated peptides makes their mass spectral detection easy and unambiguous when spiked into complex peptide mixtures. In addition, they were designed to elute sequentially over an entire aqueous to organic LC gradient and to have m/z values within the commonly scanned mass range (300-1800 Da). In a series of experiments in which these peptides were spiked into an enriched N-glycosite peptide fraction (i.e. from formerly N-glycosylated intact proteins in their deglycosylated form) isolated from human plasma, we show the utility and performance of these halogenated peptides for sample preparation and LC injection quality control as well as for retention time and mass calibration. Further use of the peptides for signal intensity normalization and retention time synchronization for selected reaction monitoring experiments is also demonstrated.
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Affiliation(s)
- Hamid Mirzaei
- Institute for Systems Biology, Seattle, Washington 98103, USA
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13
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Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 2008; 9:542. [PMID: 19087345 PMCID: PMC2651178 DOI: 10.1186/1471-2105-9-542] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 12/16/2008] [Indexed: 11/23/2022] Open
Abstract
Background Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. Results We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. Conclusion The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field.
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Affiliation(s)
- Mi-Youn Brusniak
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA.
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14
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Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M. SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 2008; 7:3470-80. [PMID: 17726677 DOI: 10.1002/pmic.200700057] [Citation(s) in RCA: 249] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Label-free quantification of high mass resolution LC-MS data has emerged as a promising technology for proteome analysis. Computational methods are required for the accurate extraction of peptide signals from LC-MS data and the tracking of these features across the measurements of different samples. We present here an open source software tool, SuperHirn, that comprises a set of modules to process LC-MS data acquired on a high resolution mass spectrometer. The program includes newly developed functionalities to analyze LC-MS data such as feature extraction and quantification, LC-MS similarity analysis, LC-MS alignment of multiple datasets, and intensity normalization. These program routines extract profiles of measured features and comprise tools for clustering and classification analysis of the profiles. SuperHirn was applied in an MS1-based profiling approach to a benchmark LC-MS dataset of complex protein mixtures with defined concentration changes. We show that the program automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile.
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Affiliation(s)
- Lukas N Mueller
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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15
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Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res 2007; 7:96-103. [PMID: 17711323 PMCID: PMC2577160 DOI: 10.1021/pr070244j] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tandem mass spectrometry (MS/MS) is frequently used in the identification of peptides and proteins. Typical proteomic experiments rely on algorithms such as SEQUEST and MASCOT to compare thousands of tandem mass spectra against the theoretical fragment ion spectra of peptides in a database. The probabilities that these spectrum-to-sequence assignments are correct can be determined by statistical software such as PeptideProphet or through estimations based on reverse or decoy databases. However, many of the software applications that assign probabilities for MS/MS spectra to sequence matches were developed using training data sets from 3D ion-trap mass spectrometers. Given the variety of types of mass spectrometers that have become commercially available over the last 5 years, we sought to generate a data set of reference data covering multiple instrumentation platforms to facilitate both the refinement of existing computational approaches and the development of novel software tools. We analyzed the proteolytic peptides in a mixture of tryptic digests of 18 proteins, named the "ISB standard protein mix", using 8 different mass spectrometers. These include linear and 3D ion traps, two quadrupole time-of-flight platforms (qq-TOF), and two MALDI-TOF-TOF platforms. The resulting data set, which has been named the Standard Protein Mix Database, consists of over 1.1 million spectra in 150+ replicate runs on the mass spectrometers. The data were inspected for quality of separation and searched using SEQUEST. All data, including the native raw instrument and mzXML formats and the PeptideProphet validated peptide assignments, are available at http://regis-web.systemsbiology.net/PublicDatasets/.
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Affiliation(s)
- John Klimek
- Institute for Systems Biology, Seattle, WA 98103
| | | | | | | | - Amelia Peterson
- Fred Hutchinson Cancer Research Center Seattle WA 98109-1024
| | | | | | | | - Parag Mallick
- Cedars-Sinai Medical Center, Los Angeles, California 90048
| | - Hookeun Lee
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Alexander Schmidt
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Reto Ossola
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Jimmy K. Eng
- Institute for Systems Biology, Seattle, WA 98103
- Fred Hutchinson Cancer Research Center Seattle WA 98109-1024
| | - Reudi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Daniel B Martin
- Institute for Systems Biology, Seattle, WA 98103
- Fred Hutchinson Cancer Research Center Seattle WA 98109-1024
- Corresponding author: Institute for Systems Biology (phone) 206 732-1365 (fax) 206 732-1299 email
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Stuart LM, Boulais J, Charriere GM, Hennessy EJ, Brunet S, Jutras I, Goyette G, Rondeau C, Letarte S, Huang H, Ye P, Morales F, Kocks C, Bader JS, Desjardins M, Ezekowitz RAB. A systems biology analysis of the Drosophila phagosome. Nature 2006; 445:95-101. [PMID: 17151602 DOI: 10.1038/nature05380] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Accepted: 10/24/2006] [Indexed: 11/08/2022]
Abstract
Phagocytes have a critical function in remodelling tissues during embryogenesis and thereafter are central effectors of immune defence. During phagocytosis, particles are internalized into 'phagosomes', organelles from which immune processes such as microbial destruction and antigen presentation are initiated. Certain pathogens have evolved mechanisms to evade the immune system and persist undetected within phagocytes, and it is therefore evident that a detailed knowledge of this process is essential to an understanding of many aspects of innate and adaptive immunity. However, despite the crucial role of phagosomes in immunity, their components and organization are not fully defined. Here we present a systems biology analysis of phagosomes isolated from cells derived from the genetically tractable model organism Drosophila melanogaster and address the complex dynamic interactions between proteins within this organelle and their involvement in particle engulfment. Proteomic analysis identified 617 proteins potentially associated with Drosophila phagosomes; these were organized by protein-protein interactions to generate the 'phagosome interactome', a detailed protein-protein interaction network of this subcellular compartment. These networks predicted both the architecture of the phagosome and putative biomodules. The contribution of each protein and complex to bacterial internalization was tested by RNA-mediated interference and identified known components of the phagocytic machinery. In addition, the prediction and validation of regulators of phagocytosis such as the 'exocyst', a macromolecular complex required for exocytosis but not previously implicated in phagocytosis, validates this strategy. In generating this 'systems-based model', we show the power of applying this approach to the study of complex cellular processes and organelles and expect that this detailed model of the phagosome will provide a new framework for studying host-pathogen interactions and innate immunity.
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Affiliation(s)
- L M Stuart
- Laboratory of Developmental Immunology, Massachusetts General Hospital/ Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, USA.
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Wilkes JG, Glover KL, Holcomb M, Rafii F, Cao X, Sutherland JB, McCarthy SA, Letarte S, Bertrand MJ. Defining and using microbial spectral databases. J Am Soc Mass Spectrom 2002; 13:875-887. [PMID: 12148811 DOI: 10.1016/s1044-0305(02)00390-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This work shows how fingerprints of mass spectral patterns from microbial isolates are affected by variations in instrumental condition, by sample environment, and by sample handling factors. It describes a novel method by which pattern distortions can be mathematically corrected for variations in factors not amenable to experimental control. One uncontrollable variable is "between-batch" differences in culture media. Another, relevant for determination of noncultured extracts, is differences between the cells' environmental experience (e.g., starved environmental extracts versus cultured standards). The method suggests that, after a single growth cycle on a solid medium (perhaps, a selective one), pyrolysis MS spectra of microbial isolates can be algorithmically compensated and an unknown isolate identified using a spectral database defined by culture on a different (perhaps, nonselective) medium. This reduces identification time to as few as 24 h from sample collection. The concept also proposes a possible way to compensate certain noncultured, nonisolated samples (e.g., cells concentrated from urine or impacted from aerosol or semi-selectively extracted by immunoaffinity methods from heavily contaminated matrices) for identification within half an hour. Using the method, microbial mass spectra from different labs can be assembled into coherent databases similar to those routinely used to identify pure compounds. This type of data treatment is applicable for rapid detection in biowarfare and bioterror events as well as in forensic, research, and clinical laboratory contexts.
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Affiliation(s)
- Jon G Wilkes
- National Center for Toxicological Research, USFDA, Jefferson, Arkansas 72079, USA.
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Lepage M, Letarte S, Michaud M, Motte-Tollet F, Hubin-Franskin MJ, Roy D, Sanche L. Electron spectroscopy of resonance-enhanced vibrational excitations of gaseous and solid tetrahydrofuran. J Chem Phys 1998. [DOI: 10.1063/1.477223] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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