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
|
Karim N, Yang Y, Salemi M, Phinney BS, Durbin-Johnson BP, Rocke DM, Rice RH. Human Keratinocyte Responses to Woodsmoke Chemicals. Chem Res Toxicol 2024; 37:675-684. [PMID: 38598786 PMCID: PMC11110105 DOI: 10.1021/acs.chemrestox.3c00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024]
Abstract
Air pollution consists of complex mixtures of chemicals with serious deleterious health effects from acute and chronic exposure. To help understand the mechanisms by which adverse effects occur, the present work examines the responses of cultured human epidermal keratinocytes to specific chemicals commonly found in woodsmoke. Our earlier findings with liquid smoke flavoring (aqueous extract of charred wood) revealed that such extracts stimulated the expression of genes associated with oxidative stress and proinflammatory response, activated the aryl hydrocarbon receptor, thereby inducing cytochrome P4501A1 activity, and induced cross-linked envelope formation, a lethal event ordinarily occurring during terminal differentiation. The present results showed that furfural produced transcriptional responses resembling those of liquid smoke, cyclohexanedione activated the aryl hydrocarbon receptor, and several chemicals induced envelope formation. Of these, syringol permeabilized the cells to the egress of lactate dehydrogenase at a concentration close to that yielding envelope formation, while furfural induced envelope formation without permeabilization detectable in this way. Furfural (but not syringol) stimulated the incorporation of amines into cell proteins in extracts in the absence of transglutaminase activity. Nevertheless, both chemicals substantially increased the amount of cellular protein incorporated into envelopes and greatly altered the envelope protein profile. Moreover, the proportion of keratin in the envelopes was dramatically increased. These findings are consistent with the chemically induced protein cross-linking in the cells. Elucidating mechanisms by which this phenomenon occurs may help understand how smoke chemicals interact with proteins to elicit cellular responses, interpret bioassays of complex pollutant mixtures, and suggest additional sensitive ways to monitor exposures.
Collapse
Affiliation(s)
- Noreen Karim
- Department
of Environmental Toxicology, University
of California Davis, Davis, California 95616-8588, United States
| | - Yatian Yang
- Department
of Environmental Toxicology, University
of California Davis, Davis, California 95616-8588, United States
| | - Michelle Salemi
- Proteomics
Core Facility, University of California
Davis, Davis, California 95616, United States
| | - Brett S. Phinney
- Proteomics
Core Facility, University of California
Davis, Davis, California 95616, United States
| | - Blythe P. Durbin-Johnson
- Division
of Biostatistics, Department of Public Health Sciences, Clinical and
Translational Science Center Biostatistics Core, University of California Davis, Davis, California 95616, United States
| | - David M. Rocke
- Division
of Biostatistics, Department of Public Health Sciences, Clinical and
Translational Science Center Biostatistics Core, University of California Davis, Davis, California 95616, United States
| | - Robert H. Rice
- Department
of Environmental Toxicology, University
of California Davis, Davis, California 95616-8588, United States
| |
Collapse
|
3
|
Mansuri MS, Bathla S, Lam TT, Nairn AC, Williams KR. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. J Proteomics 2024; 297:105109. [PMID: 38325732 PMCID: PMC10939724 DOI: 10.1016/j.jprot.2024.105109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
To identify proteins by the bottom-up mass spectrometry workflow, enzymatic digestion is essential to break down proteins into smaller peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity and generation of peptides with desirable positively charged N- and C-terminal amino acid residues that are amenable to reverse phase HPLC separation and MS/MS analyses. However, trypsin can yield variable digestion profiles and its protein cleavage activity is interdependent on trypsin source and quality, digestion time and temperature, pH, denaturant, trypsin and substrate concentrations, composition/complexity of the sample matrix, and other factors. There is therefore a need for a more standardized, general-purpose trypsin digestion protocol. Based on a review of the literature we delineate optimal conditions for carrying out trypsin digestions of complex proteomes from bulk samples to limiting amounts of protein extracts. Furthermore, we highlight recent developments and technological advances used in digestion protocols to quantify complex proteomes from single cells. SIGNIFICANCE: Currently, bottom-up MS-based proteomics is the method of choice for global proteome analysis. Since trypsin is the most utilized protease in bottom-up MS proteomics, delineating optimal conditions for carrying out trypsin digestions of complex proteomes in samples ranging from tissues to single cells should positively impact a broad range of biomedical research.
Collapse
Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA.
| |
Collapse
|
4
|
Rodzik A, Railean V, Pomastowski P, Buszewski B, Szumski M. Immobilized enzyme microreactors for analysis of tryptic peptides in β-casein and β-lactoglobulin. Sci Rep 2023; 13:16551. [PMID: 37783762 PMCID: PMC10545664 DOI: 10.1038/s41598-023-43521-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
In this study, our primary objective was to develop an effective analytical method for studying trypsin-digested peptides of two proteins commonly found in cow's milk: β-casein (βCN) and β-lactoglobulin (βLG). To achieve this, we employed two distinct approaches: traditional in-gel protein digestion and protein digestion using immobilized enzyme microreactors (μ-IMER). Both methods utilized ZipTip pipette tips filled with C18 reverse phase media for sample concentration. The μ-IMER was fabricated through a multi-step process that included preconditioning the capillary, modifying its surface, synthesizing a monolithic support, and further surface modification. Its performance was evaluated under HPLC chromatography conditions using a small-molecule trypsin substrate (BAEE). Hydrolysates from both digestion methods were analyzed using MALDI-TOF MS. Our findings indicate that the μ-IMER method demonstrated superior sequence coverage for oxidized molecules in βCN (33 ± 1.5%) and βLG (65 ± 3%) compared to classical in-gel digestion (20 ± 2% for βCN; 49 ± 2% for βLG). The use of ZipTips further improved sequence coverage in both classical in-gel digestion (26 ± 1% for βCN; 60 ± 4% for βLG) and μ-IMER (41 ± 3% for βCN; 80 ± 5% for βLG). Additionally, phosphorylations were identified. For βCN, no phosphorylation was detected using classical digestion, but the use of ZipTips showed a value of 27 ± 4%. With μ-IMER and μ-IMER-ZipTip, the values increased to 30 ± 2% and 33 ± 1%, respectively. For βLG, the use of ZipTip enabled the detection of a higher percentage of modified peptides in both classical (79 ± 2%) and μ-IMER (79 ± 4%) digestions. By providing a comprehensive comparison of traditional in-gel digestion and μ-IMER methods, this study offers valuable insights into the advantages and limitations of each approach, particularly in the context of complex biological samples. The findings set a new benchmark in protein digestion and analysis, highlighting the potential of μ-IMER systems for enhanced sequence coverage and post-translational modification detection.
Collapse
Affiliation(s)
- Agnieszka Rodzik
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland.
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland.
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland
| | - Michał Szumski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland.
| |
Collapse
|
5
|
Sundberg JP, Galantino-Homer H, Fairfield H, Ward-Bailey PF, Harris BS, Berry M, Pratt CH, Gott NE, Bechtold LS, Kaplan PR, Durbin-Johnson BP, Rocke DM, Rice RH. Witch Nails (Krt90whnl): A spontaneous mouse mutation affecting nail growth and development. PLoS One 2022; 17:e0277284. [PMID: 36374931 PMCID: PMC9662738 DOI: 10.1371/journal.pone.0277284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Numerous single gene mutations identified in humans and mice result in nail deformities with many similarities between the species. A spontaneous, autosomal, recessive mutation called witch nails (whnl) is described here where the distal nail matrix and nail bed undergo degenerative changes resulting in formation of an abnormal nail plate causing mice to develop long, curved nails. This mutation arose spontaneously in a colony of MRL/MpJ-Faslpr/J at The Jackson Laboratory. Homozygous mutant mice are recognizable by 8 weeks of age by their long, curved nails. The whnl mutation, mapped on Chromosome 15, is due to a 7-bp insertion identified in the 3’ region of exon 9 in the Krt90 gene (formerly Riken cDNA 4732456N10Rik), and is predicted to result in a frameshift that changes serine 476 to arginine and subsequently introduces 36 novel amino acids into the protein before a premature stop codon (p. Ser476ArgfsTer36). By immunohistochemistry the normal KRT90 protein is expressed in the nail matrix and nail bed in control mice where lesions are located in mutant mice. Immunoreactivity toward equine KRT124, the ortholog of mouse KRT90, is restricted to the hoof lamellae (equine hoof wall and lamellae are homologous to the mouse nail plate and nail bed) and the mouse nail bed. Equine laminitis lesions are similar to those observed in this mutant mouse suggesting that the latter may be a useful model for hoof and nail diseases. This first spontaneous mouse mutation affecting the novel Krt90 gene provides new insight into the normal regulation of the molecular pathways of nail development.
Collapse
Affiliation(s)
- John P. Sundberg
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Hannah Galantino-Homer
- New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, United States of America
| | - Heather Fairfield
- Maine Medical Center Research Institute, Scarborough, ME, United States of America
| | | | | | - Melissa Berry
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - C. Herbert Pratt
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Nicholas E. Gott
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | | | - Pauline R. Kaplan
- Department of Environmental Toxicology, University of California, Davis, CA, United States of America
| | - Blythe P. Durbin-Johnson
- Department of Applied Biosciences, University of California, Davis, CA, United States of America
| | - David M. Rocke
- Department of Applied Biosciences, University of California, Davis, CA, United States of America
| | - Robert H. Rice
- Department of Environmental Toxicology, University of California, Davis, CA, United States of America
- * E-mail:
| |
Collapse
|
6
|
Segl M, Stutz H. Bottom-Up Analysis of Proteins by Peptide Mass Fingerprinting with tCITP-CZE-ESI-TOF MS After Tryptic Digest. Methods Mol Biol 2022; 2531:93-106. [PMID: 35941481 DOI: 10.1007/978-1-0716-2493-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification of proteins in samples of moderate to complex composition is primarily done by bottom-up approaches. Therefore, proteins are enzymatically digested, mostly by trypsin, and the resulting peptides are then separated prior to their transfer to a mass spectrometer. The following protocol portrays a bottom-up method, which was optimized for the application of CZE-ESI-TOF MS. Protein denaturation is achieved by addition of 2,2,2-trifluoroethanol (TFE) and heat treatment. Afterwards, disulfide bonds are reduced with tris-(2-carboxyethyl)phosphine (TCEP) and subsequently alkylated with iodoacetamide (IAA). The tryptic digest is performed in an ammonium bicarbonate buffer at pH 8.0. The digested protein sample is then concentrated in-capillary by transient capillary isotachophoresis (tCITP) with subsequent CZE separation of tryptic peptides in an acidic background electrolyte. Hyphenation to a time-of-flight (TOF) mass spectrometer is carried out by a triple-tube coaxial sheath flow interface, which uses electrospray ionization (ESI). Peptide identification is done by peptide mass fingerprinting (PMF). The protocol is outlined exemplarily for a model protein, i.e., bovine β-lactoglobulin A.
Collapse
Affiliation(s)
- Marius Segl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Salzburg, Austria
| | - Hanno Stutz
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Salzburg, Austria.
| |
Collapse
|
7
|
Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
Collapse
Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
8
|
Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
Collapse
|
9
|
Rabe A, Gesell Salazar M, Völker U. Bottom-Up Community Proteome Analysis of Saliva Samples and Tongue Swabs by Data-Dependent Acquisition Nano LC-MS/MS Mass Spectrometry. Methods Mol Biol 2021; 2327:221-238. [PMID: 34410648 DOI: 10.1007/978-1-0716-1518-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis using mass spectrometry enables the characterization of metaproteomes in their native environments and overcomes the limitation of proteomics of pure cultures. Metaproteomics is a promising approach to link functions of currently actively expressed genes to the phylogenetic composition of the microbiome in their habitat. In this chapter, we describe the preparation of saliva samples and tongue swabs for nLC-MS/MS measurements and their bioinformatic analysis based on the Trans-Proteomic Pipeline and Prophane to study the oral microbiome .
Collapse
Affiliation(s)
- Alexander Rabe
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
| | - Manuela Gesell Salazar
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
10
|
Goecker ZC, Salemi MR, Karim N, Phinney BS, Rice RH, Parker GJ. Optimal processing for proteomic genotyping of single human hairs. Forensic Sci Int Genet 2020; 47:102314. [DOI: 10.1016/j.fsigen.2020.102314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/25/2020] [Accepted: 05/15/2020] [Indexed: 01/08/2023]
|
11
|
Ramirez-Rodriguez EA, Heazlewood JL. Enrichment of N-Linked Glycopeptides and Their Identification by Complementary Fragmentation Techniques. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2139:225-240. [PMID: 32462590 DOI: 10.1007/978-1-0716-0528-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
N-linked glycans are a ubiquitous posttranslational modification and are essential for correct protein folding in the endoplasmic reticulum of plants. However, this likely represents a narrow functional role for the diverse array of glycan structures currently associated with N-glycoproteins in plants. The identification of N-linked glycosylation sites and their structural characterization by mass spectrometry remains challenging due to their size, relative abundance, structural heterogeneity, and polarity. Current proteomic workflows are not optimized for the enrichment, identification and characterization of N-glycopeptides. Here we describe a detailed analytical procedure employing hydrophilic interaction chromatography enrichment, high-resolution tandem mass spectrometry employing complementary fragmentation techniques (higher-energy collisional dissociation and electron-transfer dissociation) and a data analytics workflow to produce an unbiased high confidence N-glycopeptide profile from plant samples.
Collapse
Affiliation(s)
| | - Joshua L Heazlewood
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
12
|
Jaeger K, Sukseree S, Zhong S, Phinney BS, Mlitz V, Buchberger M, Narzt MS, Gruber F, Tschachler E, Rice RH, Eckhart L. Cornification of nail keratinocytes requires autophagy for bulk degradation of intracellular proteins while sparing components of the cytoskeleton. Apoptosis 2020; 24:62-73. [PMID: 30552537 PMCID: PMC6373260 DOI: 10.1007/s10495-018-1505-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Epidermal keratinocytes undergo cornification to form the cellular building blocks of hard skin appendages such as nails and the protective layer on the surface of the skin. Cornification requires the cross-linking of structural proteins and the removal of other cellular components to form mechanically rigid and inert corneocytes. Autophagy has been proposed to contribute to this intracellular remodelling process, but its molecular targets in keratinocytes, if any, have remained elusive. Here, we deleted the essential autophagy factor Atg7 in K14-positive epithelia of mice and determined by proteomics the impact of this deletion on the abundance of individual proteins in cornified nails. The genetic suppression of autophagy in keratinocytes resulted in a significant increase in the number of proteins that survived cornification and in alterations of their abundance in the nail proteome. A broad range of enzymes and other non-structural proteins were elevated whereas the amounts of cytoskeletal proteins of the keratin and keratin-associated protein families, cytolinker proteins and desmosomal proteins were either unaltered or decreased in nails of mice lacking epithelial autophagy. Among the various types of non-cytoskeletal proteins, the subunits of the proteasome and of the TRiC/CCT chaperonin were most strongly elevated in mutant nails, indicating a particularly important role of autophagy in removing these large protein complexes during normal cornification. Taken together, the results of this study suggest that autophagy is active during nail keratinocyte cornification and its substrate specificity depends on the accessibility of proteins outside of the cytoskeleton and their presence in large complexes.
Collapse
Affiliation(s)
- Karin Jaeger
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria
| | - Supawadee Sukseree
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria
| | - Shaomin Zhong
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria
| | - Brett S Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA, USA
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria
| | - Maria Buchberger
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria
| | - Marie Sophie Narzt
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria.,Christian Doppler Laboratory on Biotechnology of Skin Aging, Vienna, Austria
| | - Florian Gruber
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria.,Christian Doppler Laboratory on Biotechnology of Skin Aging, Vienna, Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria
| | - Robert H Rice
- Department of Environmental Toxicology, University of California, One Shields Avenue, Davis, CA, 95616-8588, USA.
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria.
| |
Collapse
|
13
|
Moons J, Azambuja F, Mihailovic J, Kozma K, Smiljanic K, Amiri M, Cirkovic Velickovic T, Nyman M, Parac‐Vogt TN. Discrete Hf
18
Metal‐oxo Cluster as a Heterogeneous Nanozyme for Site‐Specific Proteolysis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jens Moons
- Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Francisco Azambuja
- Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Leuven Belgium
| | - Jelena Mihailovic
- Faculty of Chemistry University of Belgrade Studentski trg 16 11000 Belgrade Serbia
| | - Karoly Kozma
- Department of Chemistry Oregon State University Corvallis OR 97331-4003 USA
| | - Katarina Smiljanic
- Faculty of Chemistry University of Belgrade Studentski trg 16 11000 Belgrade Serbia
| | - Mehran Amiri
- Department of Chemistry Oregon State University Corvallis OR 97331-4003 USA
| | - Tanja Cirkovic Velickovic
- Faculty of Chemistry University of Belgrade Studentski trg 16 11000 Belgrade Serbia
- Ghent University Global Campus Incheon South Korea
- Ghent University Faculty of Bioscience Engineering Ghent Belgium
- Serbian Academy of Sciences and Arts Belgrade Serbia
| | - May Nyman
- Department of Chemistry Oregon State University Corvallis OR 97331-4003 USA
| | | |
Collapse
|
14
|
Moons J, de Azambuja F, Mihailovic J, Kozma K, Smiljanic K, Amiri M, Cirkovic Velickovic T, Nyman M, Parac-Vogt TN. Discrete Hf 18 Metal-oxo Cluster as a Heterogeneous Nanozyme for Site-Specific Proteolysis. Angew Chem Int Ed Engl 2020; 59:9094-9101. [PMID: 32154631 DOI: 10.1002/anie.202001036] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/04/2020] [Indexed: 12/11/2022]
Abstract
The selective hydrolysis of proteins by non-enzymatic catalysis is difficult to achieve, yet it is crucial for applications in biotechnology and proteomics. Herein, we report that discrete hafnium metal-oxo cluster [Hf18 O10 (OH)26 (SO4 )13 ⋅(H2 O)33 ] (Hf18 ), which is centred by the same hexamer motif found in many MOFs, acts as a heterogeneous catalyst for the efficient hydrolysis of horse heart myoglobin (HHM) in low buffer concentrations. Among 154 amino acids present in the sequence of HHM, strictly selective cleavage at only 6 solvent accessible aspartate residues was observed. Mechanistic experiments suggest that the hydrolytic activity is likely derived from the actuation of HfIV Lewis acidic sites and the Brønsted acidic surface of Hf18 . X-ray scattering and ESI-MS revealed that Hf18 is completely insoluble in these conditions, confirming the HHM hydrolysis is caused by a heterogeneous reaction of the solid Hf18 cluster, and not from smaller, soluble Hf species that could leach into solution.
Collapse
Affiliation(s)
- Jens Moons
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | | | - Jelena Mihailovic
- Faculty of Chemistry, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - Karoly Kozma
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331-4003, USA
| | - Katarina Smiljanic
- Faculty of Chemistry, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - Mehran Amiri
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331-4003, USA
| | - Tanja Cirkovic Velickovic
- Faculty of Chemistry, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.,Ghent University Global Campus, Incheon, South Korea.,Ghent University, Faculty of Bioscience Engineering, Ghent, Belgium.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - May Nyman
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331-4003, USA
| | | |
Collapse
|
15
|
Catlin LA, Chou RM, Goecker ZC, Mullins LA, Silva DSBSS, Spurbeck RR, Parker GJ, Bartling CM. Demonstration of a mitochondrial DNA-compatible workflow for genetically variant peptide identification from human hair samples. Forensic Sci Int Genet 2019; 43:102148. [DOI: 10.1016/j.fsigen.2019.102148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Accepted: 08/14/2019] [Indexed: 12/01/2022]
|
16
|
|
17
|
Borja T, Karim N, Goecker Z, Salemi M, Phinney B, Naeem M, Rice R, Parker G. Proteomic genotyping of fingermark donors with genetically variant peptides. Forensic Sci Int Genet 2019; 42:21-30. [DOI: 10.1016/j.fsigen.2019.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/09/2019] [Accepted: 05/26/2019] [Indexed: 01/31/2023]
|
18
|
Zhang J, Zhao M, Xiao W, Chang L, Wang F, Xu P. Recombinant expression, purification and characterization of acetylated LysargiNase from Escherichia coli with high activity and stability. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1067-1075. [PMID: 30900783 DOI: 10.1002/rcm.8440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE LysargiNase is a novel characterized metalloprotease that can cleave the N-terminii of lysine or arginine residues. The peptides generated by LysargiNase are just mirrors to those generated by trypsin. These characteristics of LysargiNase provide a powerful tool for mass spectrometry (MS)-based proteomics research. A highly active and stable LysargiNase produced by an easy and inexpensive method could greatly benefit proteomics research. Here, we report the soluble recombinant expression, purification and acetyl modification of LysargiNase in Escherichia coli. METHODS The coding sequence of LysargiNase with an enterokinase cleavage site at the N-terminus was inserted into plasmid pGEX-4 T-2 and transformed into E. coli BL21 (DE3). The strain was cultured in a 14-L fermenter with a working volume of 5 L. The protein expression was induced by adding isopropyl-β-D-thiogalactoside (IPTG) to a final concentration of 1 mM. The recombinant LysargiNase was loaded onto a GSTrap and an on-column digestion was performed to remove the GST tag and was subsequently purified by chromatographic purification. In vitro acetylation of LysargiNase was performed by using acetic anhydride. The digestion efficiency and specificity of recombinant LysargiNase and acetylated LysargiNase were compared with simple protein substrate, human serum albumin (HSA), and a complex proteomic sample, yeast lysate, by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). RESULTS Highly soluble expression of recombinant LysargiNase was achieved by plasmid pGEX-4 T-2 in E. coli BL21 (DE3). In addition, acetylation of purified LysargiNase significantly increased its resistance to autolysis, which resulted in a more complete digestion of proteomics samples and more identified peptides and proteins by LC/MS/MS. CONCLUSIONS In this study, we constructed a highly soluble expression system for producing recombinant LysargiNase in E. coli, which gave tremendous advantages in the downstream purification process. We also confirmed that acetyl modification can increase the stability and activity of recombinant LysargiNase. The study provided a superior way to produce this powerful tool for proteomics research.
Collapse
Affiliation(s)
- Junling Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Mingzhi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Weidi Xiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Fuqiang Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) and Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
- Guizhou University School of Medicine, Guiyang, 550025, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan, 430072, China
| |
Collapse
|
19
|
Heissel S, Frederiksen SJ, Bunkenborg J, Højrup P. Enhanced trypsin on a budget: Stabilization, purification and high-temperature application of inexpensive commercial trypsin for proteomics applications. PLoS One 2019; 14:e0218374. [PMID: 31246970 PMCID: PMC6597055 DOI: 10.1371/journal.pone.0218374] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/02/2019] [Indexed: 01/22/2023] Open
Abstract
Trypsin is by far the most commonly used protease in proteomics. Even though the amount of protease used in each experiment is very small, digestion of large amounts of protein prior to enrichment can be rather costly. The price of commercial trypsin is highly dependent on the quality of the enzyme, which is determined by its purity, activity, and chemical modifications. In this study we evaluated several strategies for improving the quality of crude trypsin by reductive methylation and affinity purification. We present a protocol applicable to most proteomics laboratories for obtaining a highly stable and pure trypsin preparation using reductive methylation and purification by benzamidine-sepharose. The entire workflow can be performed within a day and yields ~4 mg per batch but is completely scalable. The methylated product was benchmarked against sequencing grade trypsin from Promega and they were found to be comparable for one hour digestions at elevated temperatures, where residual chymotryptic activity was found to be negligible.
Collapse
Affiliation(s)
- Søren Heissel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Sigurd J. Frederiksen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | | | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- * E-mail:
| |
Collapse
|
20
|
El Amrani M, Donners AAM, Hack CE, Huitema ADR, van Maarseveen EM. Six-step workflow for the quantification of therapeutic monoclonal antibodies in biological matrices with liquid chromatography mass spectrometry - A tutorial. Anal Chim Acta 2019; 1080:22-34. [PMID: 31409472 DOI: 10.1016/j.aca.2019.05.076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 01/07/2023]
Abstract
The promising pipeline of therapeutic monoclonal antibodies (mAbs) demands robust bioanalytical methods with swift development times for pharmacokinetic studies. Over the past decades ligand binding assays were the methods of choice for absolute quantification. However, the production of the required anti-idiotypic antibodies and ligands limits high-throughput method development for sensitive, accurate, and reproducible quantification of therapeutic mAbs. In recent years, high-resolution liquid chromatography tandem mass-spectrometry (LC-MS) systems have enabled absolute quantification of therapeutic mAbs with short method development times. These systems have additional benefits, such as a large linear dynamic range, a high specificity and the option of multiplexing. Here, we briefly discuss the current strategies for the quantification of therapeutic mAbs in biological matrices using LC-MS analysis based on top-down and middle-down quantitative proteomics. Then, we present the widely used bottom-up method in a six-step workflow, which can be used as guidance for quantitative LC-MS/MS method development of mAbs. Finally, strengths and weaknesses of the bottom-up method, which currently provides the most benefits, are discussed in detail.
Collapse
Affiliation(s)
- Mohsin El Amrani
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Anouk A M Donners
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - C Erik Hack
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Alwin D R Huitema
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Erik M van Maarseveen
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands. https://www.umcutrecht.nl
| |
Collapse
|
21
|
Karim N, Durbin-Johnson B, Rocke DM, Salemi M, Phinney BS, Naeem M, Rice RH. Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis. J Proteomics 2019; 201:104-109. [DOI: 10.1016/j.jprot.2019.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/22/2019] [Accepted: 04/07/2019] [Indexed: 02/06/2023]
|
22
|
Kjellander M, Billinger E, Ramachandraiah H, Boman M, Bergström Lind S, Johansson G. A flow-through nanoporous alumina trypsin bioreactor for mass spectrometry peptide fingerprinting. J Proteomics 2018; 172:165-172. [PMID: 28942014 DOI: 10.1016/j.jprot.2017.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/31/2017] [Accepted: 09/16/2017] [Indexed: 11/29/2022]
Abstract
Mass spectrometry-based proteomics benefits from efficient digestion of protein samples. In this study, trypsin was immobilized on nanoporous anodized alumina membranes to create an enzyme reactor suitable for peptide mass fingerprinting. The membranes were derivatized with 3-aminopropyltriethoxysilane and the amino groups were activated with carbonyldiimidazole to allow coupling of porcine trypsin via ε-amino groups. The function was assessed using the artificial substrate Nα-Benzoyl-L-arginine 4-nitroanilide hydrochloride, bovine ribonuclease A and a human plasma sample. A 10-membrane flow-through reactor was used for fragmentation and MS analysis after a single pass of substrate both by collection of product and subsequent off-line analysis, and by coupling on-line to the instrument. The peptide pattern allowed correct identification of the single target protein in both cases, and of >70 plasma proteins in single pass mode followed by LC-MS analysis. The reactor retained 76% of the initial activity after 14days of storage and repeated use at room temperature. SIGNIFICANCE This manuscript describes the design of a stable enzyme reactor that allows efficient and fast digestion with negligible leakage of enzyme and enzyme fragments. The high stability facilitates the use in an online-setup with MS detection since it allows the processing of multiple samples within an extended period of time without replacement.
Collapse
Affiliation(s)
- Marcus Kjellander
- Dept. of Chemistry-BMC, Uppsala University, BMC, Husargatan 3, Box 576, SE-75123 Uppsala, Sweden
| | - Erika Billinger
- Dept. of Chemistry-BMC, Uppsala University, BMC, Husargatan 3, Box 576, SE-75123 Uppsala, Sweden
| | - Harisha Ramachandraiah
- Dept. of Chemistry-BMC, Uppsala University, BMC, Husargatan 3, Box 576, SE-75123 Uppsala, Sweden
| | - Mats Boman
- Dept. of Chemistry-Ångström, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, Box 538, SE-75121 Uppsala, Sweden
| | - Sara Bergström Lind
- Dept. of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gunnar Johansson
- Dept. of Chemistry-BMC, Uppsala University, BMC, Husargatan 3, Box 576, SE-75123 Uppsala, Sweden.
| |
Collapse
|
23
|
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]
|
24
|
Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, Parker GJ, Rice RH. Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides. Proteomics 2017; 17. [PMID: 28544375 DOI: 10.1002/pmic.201600462] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/03/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]
Abstract
Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from ten pairs of monozygotic twins. Profiling using the protein tryptic digests revealed that samples from identical twins had typically an order of magnitude fewer protein expression differences than unrelated individuals. The data did not indicate that the degree of difference within twin pairs increased with age. In parallel, data from the digests were used to detect genetically variant peptides that result from common nonsynonymous single nucleotide polymorphisms in genes expressed in the hair follicle. Compilation of the variants permitted sorting of the samples by hierarchical clustering, permitting accurate matching of twin pairs. The results demonstrate that genetic differences are detectable by proteomic methods and provide a framework for developing quantitative statistical estimates of personal identification that increase the value of hair shaft evidence.
Collapse
Affiliation(s)
- Pei-Wen Wu
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Katelyn E Mason
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, CA, USA
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, CA, USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - Glendon J Parker
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, CA, USA.,Protein-Based Identification Technologies, Orem, UT, USA
| | - Robert H Rice
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California, Davis, CA, USA
| |
Collapse
|
25
|
Qin G, Ma J, Chen X, Chu Z, She YM. Methylated-antibody affinity purification to improve proteomic identification of plant RNA polymerase Pol V complex and the interacting proteins. Sci Rep 2017; 7:42943. [PMID: 28224978 PMCID: PMC5320500 DOI: 10.1038/srep42943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022] Open
Abstract
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C. By this method, the antibody remains intact and does not interfere with the downstream identification of interacting proteins. Non-specific binding proteins were excluded using 14N/15N-metabolic labeling of wild-type and the transgenic plant counterparts. The method was employed to identify 12 co-immunoprecipitated protein subunits in Pol V complex and to discover 17 potential interacting protein targets in Arabidopsis. Our results demonstrated that the modification of antibodies by reductive dimethylation can improve the reliability and sensitivity of identifying low-abundance proteins through on-bead digestion and mass spectrometry. We also show that coupling this technique with chemical crosslinking enables in-depth characterization of endogenous protein complexes and the protein-protein interaction networks including mapping the surface topology and post-translational modifications of interacting proteins.
Collapse
Affiliation(s)
- Guochen Qin
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Jun Ma
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Xiaomei Chen
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Zhaoqing Chu
- Shanghai Chenshan Plant Science Research Center and Shanghai Chenshan Botanic Garden, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Yi-Min She
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China.,Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| |
Collapse
|
26
|
Rizzo DG, Prentice BM, Moore JL, Norris JL, Caprioli RM. Enhanced Spatially Resolved Proteomics Using On-Tissue Hydrogel-Mediated Protein Digestion. Anal Chem 2017; 89:2948-2955. [DOI: 10.1021/acs.analchem.6b04395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David G. Rizzo
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boone M. Prentice
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jessica L. Moore
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeremy L. Norris
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|
27
|
Grebe SK, Singh RJ. Clinical peptide and protein quantification by mass spectrometry (MS). Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
28
|
Banar M, Emaneini M, Satarzadeh M, Abdellahi N, Beigverdi R, van Leeuwen WB, Jabalameli F. Evaluation of Mannosidase and Trypsin Enzymes Effects on Biofilm Production of Pseudomonas aeruginosa Isolated from Burn Wound Infections. PLoS One 2016; 11:e0164622. [PMID: 27736961 PMCID: PMC5063459 DOI: 10.1371/journal.pone.0164622] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/28/2016] [Indexed: 11/29/2022] Open
Abstract
Biofilm is an important virulence factor in Pseudomonas aeruginosa and has a substantial role in antibiotic resistance and chronic burn wound infections. New therapeutic agents against P. aeruginosa, degrading biofilms in burn wounds and improving the efficacy of current antimicrobial agents, are required. In this study, the effects of α-mannosidase, β-mannosidase and trypsin enzymes on the degradation of P. aeruginosa biofilms and on the reduction of ceftazidime minimum biofilm eliminating concentrations (MBEC) were evaluated. All tested enzymes, destroyed the biofilms and reduced the ceftazidime MBECs. However, only trypsin had no cytotoxic effect on A-431 human epidermoid carcinoma cell lines. In conclusion, since trypsin had better features than mannosidase enzymes, it can be a promising agent in combatting P. aeruginosa burn wound infections.
Collapse
Affiliation(s)
- Maryam Banar
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Nafiseh Abdellahi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Willem B. van Leeuwen
- Department of Medical Microbiology & Infectious Diseases. Erasmus Medical Center, University of Applied Sciences, Leiden, Netherlands
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- * E-mail:
| |
Collapse
|
29
|
Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi M, Phinney BS, Rocke DM, Roop DR. Proteomic Analysis of Loricrin Knockout Mouse Epidermis. J Proteome Res 2016; 15:2560-6. [PMID: 27418529 DOI: 10.1021/acs.jproteome.6b00108] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The crosslinked envelope of the mammalian epidermal corneocyte serves as a scaffold for assembly of the lipid barrier of the epidermis. Thus, deficient envelope crosslinking by keratinocyte transglutaminase (TGM1) is a major cause of the human autosomal recessive congenital ichthyoses characterized by barrier defects. Expectations that loss of some envelope protein components would also confer an ichthyosis phenotype have been difficult to demonstrate. To help rationalize this observation, the protein profile of epidermis from loricrin knockout mice has been compared to that of wild type. Despite the mild phenotype of the knockout, some 40 proteins were incorporated into envelope material to significantly different extents compared to those of wild type. Nearly half were also incorporated to similarly altered extents into the disulfide bonded keratin network of the corneocyte. The results suggest that loss of loricrin alters their incorporation into envelopes as a consequence of protein-protein interactions during cell maturation. Mass spectrometric protein profiling revealed that keratin 1, keratin 10, and loricrin are prominent envelope components and that dozens of other proteins are also components. This finding helps rationalize the potential formation of functional envelopes, despite loss of a single component, due to the availability of many alternative transglutaminase substrates.
Collapse
Affiliation(s)
| | | | - Yosuke Ishitsuka
- Department of Dermatology, Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | | | | | | | - Dennis R Roop
- Department of Dermatology, Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
| |
Collapse
|
30
|
Wu F, Zhao M, Zhang Y, Su N, Xiong Z, Xu P. Recombinant acetylated trypsin demonstrates superior stability and higher activity than commercial products in quantitative proteomics studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1059-1066. [PMID: 27003043 DOI: 10.1002/rcm.7535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/31/2016] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Trypsin is an important digestive enzyme in peptide sample preparation for proteomics. It digests proteins at the C-terminal of Arg or Lys residues. The majority of commercial products are obtained from animal sources. In a previous study, we reported the production process for recombinant trypsin (r-trypsin) and acetylated trypsin (r-Ac-trypsin). In this paper, we want to evaluate whether the r-trypsin and r-Ac-trypsin are suitable for proteomics research. METHODS The trypsins used in this research were first normalized to the same concentration and used for further evaluation. The stability and buffer compatibility (2M urea, 0.1% SDS and 10% acetonitrile) were compared and visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The digestion efficiency and specificity were compared based on a simple protein substrate, human serum albumin (HSA) and a complex proteomic sample, yeast lysate. The acquisition of proteomics data was achieved by ultra-high performance liquid chromatography (UPLC) connected to an LTQ Orbitrap Velos mass spectrometer. RESULTS r-Ac-trypsin demonstrated similar tolerance to 2 M urea and 10% acetonitrile but weaker 0.1% SDS tolerance than commercial trypsins. Based on simple protein sample HSA, the activity and specificity of r-Ac-trypsin were similar to that of commercial trypsins. However, it demonstrated superior activity and specificity on complicated samples like yeast lysate. More interestingly, the newly developed r-Ac-trypsin was more resistant to autolysis, which enabled more complete digestion of proteomic samples. CONCLUSIONS The r-Ac-trypsin described here is a recombinant product. In addition it showed similar or superior properties such as stability activity and specificity to commercial products. It can be used in peptide sample preparation in proteomics studies.
Collapse
Affiliation(s)
- Feilin Wu
- Life Science College, Southwest Forestry University, Kunming, 650224, P.R. China
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Mingzhi Zhao
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Yao Zhang
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
- Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Su
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Zhi Xiong
- Life Science College, Southwest Forestry University, Kunming, 650224, P.R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P.R. China
- Anhui Medical University, Hefei, 230032, Anhui, P.R. China
| |
Collapse
|
31
|
Schittmayer M, Fritz K, Liesinger L, Griss J, Birner-Gruenberger R. Cleaning out the Litterbox of Proteomic Scientists' Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts. J Proteome Res 2016; 15:1222-9. [PMID: 26938934 PMCID: PMC4820788 DOI: 10.1021/acs.jproteome.5b01105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Chemically
modified trypsin is a standard reagent in proteomics
experiments but is usually not considered in database searches. Modification
of trypsin is supposed to protect the protease against autolysis and
the resulting loss of activity. Here, we show that modified trypsin
is still subject to self-digestion, and, as a result, modified trypsin-derived
peptides are present in standard digests. We depict that these peptides
commonly lead to false-positive assignments even if native trypsin
is considered in the database. Moreover, we present an easily implementable
method to include modified trypsin in the database search with a minimal
increase in search time and search space while efficiently avoiding
these false-positive hits.
Collapse
Affiliation(s)
- Matthias Schittmayer
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , 8010 Graz, Austria.,Omics Center Graz, BioTechMed-Graz , 8010 Graz, Austria
| | - Katarina Fritz
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , 8010 Graz, Austria.,Omics Center Graz, BioTechMed-Graz , 8010 Graz, Austria
| | - Laura Liesinger
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , 8010 Graz, Austria.,Omics Center Graz, BioTechMed-Graz , 8010 Graz, Austria
| | - Johannes Griss
- Department of Dermatology, Medical University of Vienna , 1090 Vienna, Austria
| | - Ruth Birner-Gruenberger
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , 8010 Graz, Austria.,Omics Center Graz, BioTechMed-Graz , 8010 Graz, Austria
| |
Collapse
|
32
|
Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
Collapse
Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
| |
Collapse
|
33
|
Phillips MA, Cánovas A, Wu PW, Islas-Trejo A, Medrano JF, Rice RH. Parallel responses of human epidermal keratinocytes to inorganic SbIII and AsIII. ENVIRONMENTAL CHEMISTRY (COLLINGWOOD, VIC.) 2016; 13:963-970. [PMID: 28713220 PMCID: PMC5507681 DOI: 10.1071/en16019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
SbIII and AsIII are known to exhibit similar chemical properties, but the degree of similarity in their effects on biological systems merits further exploration. Present work compares the responses of human epidermal keratinocytes, a known target cell type for arsenite-induced carcinogenicity, to these metalloids after treatment for a week at environmentally relevant concentrations. Previous work with these cells has shown that arsenite and antimonite have parallel effects in suppressing differentiation, altering levels of several critical enzymes and maintaining colony forming ability. More globally, protein profiling now reveals parallels in SbIII and AsIII effects. The more sensitive technique of transcriptional profiling also shows considerable parallels. Thus, gene expression changes were almost entirely in the same directions for the two treatments, although the degree of change was sometimes significantly different. Inspection of the changes revealed that RYR1 and LRIG1 were among the genes strongly suppressed, consistent with reduced calcium-dependent differentiation and maintenance of EGF-dependent proliferative potential. Moreover, levels of miRNAs in the cells were altered in parallel, with nearly 90% of the 198 most highly expressed ones being suppressed. Among these was miR-203, which is known to decrease proliferative potential. Finally, both SbIII and AsIII were seen to attenuate bone morphogenetic protein 6 induction of dual specificity phosphatases 2 and 14, consistent with maintaining epidermal growth factor receptor signaling. These findings raise the question whether SbIII, like AsIII, could act as a human skin carcinogen.
Collapse
Affiliation(s)
- Marjorie A. Phillips
- Department of Environmental Toxicology, University of California, Davis, CA 95616
| | - Angela Cánovas
- Department of Animal Science, University of California, Davis, CA 95616
| | - Pei-Wen Wu
- Department of Environmental Toxicology, University of California, Davis, CA 95616
| | - Alma Islas-Trejo
- Department of Animal Science, University of California, Davis, CA 95616
| | - Juan F. Medrano
- Department of Animal Science, University of California, Davis, CA 95616
| | - Robert H. Rice
- Department of Environmental Toxicology, University of California, Davis, CA 95616
| |
Collapse
|
34
|
Development of Monolithic Column Materials for the Separation and Analysis of Glycans. CHROMATOGRAPHY 2015. [DOI: 10.3390/chromatography2010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
35
|
Cao YA, Hickerson RP, Seegmiller BL, Grapov D, Gross MM, Bessette MR, Phinney BS, Flores MA, Speaker TJ, Vermeulen A, Bravo AA, Bruckner AL, Milstone LM, Schwartz ME, Rice RH, Kaspar RL. Gene expression profiling in pachyonychia congenita skin. J Dermatol Sci 2015; 77:156-65. [PMID: 25656049 DOI: 10.1016/j.jdermsci.2015.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND Pachyonychia congenita (PC) is a skin disorder resulting from mutations in keratin (K) proteins including K6a, K6b, K16, and K17. One of the major symptoms is painful plantar keratoderma. The pathogenic sequelae resulting from the keratin mutations remain unclear. OBJECTIVE To better understand PC pathogenesis. METHODS RNA profiling was performed on biopsies taken from PC-involved and uninvolved plantar skin of seven genotyped PC patients (two K6a, one K6b, three K16, and one K17) as well as from control volunteers. Protein profiling was generated from tape-stripping samples. RESULTS A comparison of PC-involved skin biopsies to adjacent uninvolved plantar skin identified 112 differentially-expressed mRNAs common to patient groups harboring K6 (i.e., both K6a and K6b) and K16 mutations. Among these mRNAs, 25 encode structural proteins including keratins, small proline-rich and late cornified envelope proteins, 20 are related to metabolism and 16 encode proteases, peptidases, and their inhibitors including kallikrein-related peptidases (KLKs), and serine protease inhibitors (SERPINs). mRNAs were also identified to be differentially expressed only in K6 (81) or K16 (141) patient samples. Furthermore, 13 mRNAs were identified that may be involved in pain including nociception and neuropathy. Protein profiling, comparing three K6a plantar tape-stripping samples to non-PC controls, showed changes in the PC corneocytes similar, but not identical, to the mRNA analysis. CONCLUSION Many differentially-expressed genes identified in PC-involved skin encode components critical for skin barrier homeostasis including keratinocyte proliferation, differentiation, cornification, and desquamation. The profiling data provide a foundation for unraveling the pathogenesis of PC and identifying targets for developing effective PC therapeutics.
Collapse
Affiliation(s)
- Yu-An Cao
- TransDerm Inc., Santa Cruz, CA 95060, USA
| | | | | | - Dmitry Grapov
- University of California at Davis, Davis, CA 95616, USA
| | - Maren M Gross
- Dharmacon part of GE Healthcare, Lafayette, CO 80026, USA
| | | | | | | | | | | | - Albert A Bravo
- Podiatric Medicine and Surgery, Pittsfield, MA 01201, USA
| | - Anna L Bruckner
- University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Mary E Schwartz
- Pachyonychia Congenita Project, Salt Lake City, UT 84109, USA
| | - Robert H Rice
- University of California at Davis, Davis, CA 95616, USA
| | | |
Collapse
|
36
|
Hu M, Liu Y, Yu K, Liu X. Decreasing the amount of trypsin in in-gel digestion leads to diminished chemical noise and improved protein identifications. J Proteomics 2014; 109:16-25. [DOI: 10.1016/j.jprot.2014.06.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/13/2014] [Accepted: 06/20/2014] [Indexed: 11/26/2022]
|
37
|
Laatsch CN, Durbin-Johnson BP, Rocke DM, Mukwana S, Newland AB, Flagler MJ, Davis MG, Eigenheer RA, Phinney BS, Rice RH. Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis. PeerJ 2014; 2:e506. [PMID: 25165623 PMCID: PMC4137660 DOI: 10.7717/peerj.506] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/18/2014] [Indexed: 12/22/2022] Open
Abstract
Hair from different individuals can be distinguished by physical properties. Although some data exist on other species, examination of the individual molecular differences within the human hair shaft has not been thoroughly investigated. Shotgun proteomic analysis revealed considerable variation in profile among samples from Caucasian, African–American, Kenyan and Korean subjects. Within these ethnic groups, prominent keratin proteins served to distinguish individual profiles. Differences between ethnic groups, less marked, relied to a large extent on levels of keratin associated proteins. In samples from Caucasian subjects, hair shafts from axillary, beard, pubic and scalp regions exhibited distinguishable profiles, with the last being most different from the others. Finally, the profile of isolated hair cuticle cells was distinguished from that of total hair shaft by levels of more than 20 proteins, the majority of which were prominent keratins. The cuticle also exhibited relatively high levels of epidermal transglutaminase (TGM3), accounting for its observed low degree of protein extraction by denaturants. In addition to providing insight into hair structure, present findings may lead to improvements in differentiating hair from various ethnic origins and offer an approach to extending use of hair in crime scene evidence for distinguishing among individuals.
Collapse
Affiliation(s)
- Chelsea N Laatsch
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California , Davis, CA , USA
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California , Davis, CA , USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California , Davis, CA , USA
| | | | - Abby B Newland
- Procter & Gamble, Mason Business Center , Mason, OH , USA
| | | | | | | | - Brett S Phinney
- Proteomics Core Facility, University of California , Davis, CA , USA
| | - Robert H Rice
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California , Davis, CA , USA
| |
Collapse
|
38
|
|
39
|
Vandermarliere E, Mueller M, Martens L. Getting intimate with trypsin, the leading protease in proteomics. MASS SPECTROMETRY REVIEWS 2013; 32:453-65. [PMID: 23775586 DOI: 10.1002/mas.21376] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/15/2013] [Accepted: 02/15/2013] [Indexed: 05/21/2023]
Abstract
Nowadays, mass spectrometry-based proteomics is carried out primarily in a bottom-up fashion, with peptides obtained after proteolytic digest of a whole proteome lysate as the primary analytes instead of the proteins themselves. This experimental setup crucially relies on a protease to digest an abundant and complex protein mixture into a far more complex peptide mixture. Full knowledge of the working mechanism and specificity of the used proteases is therefore crucial, both for the digestion step itself as well as for the downstream identification and quantification of the (fragmentation) mass spectra acquired for the peptides in the mixture. Targeted protein analysis through selected reaction monitoring, a relative newcomer in the specific field of mass spectrometry-based proteomics, even requires a priori understanding of protease behavior for the proteins of interest. Because of the rapidly increasing popularity of proteomics as an analytical tool in the life sciences, there is now a renewed demand for detailed knowledge on trypsin, the workhorse protease in proteomics. This review addresses this need and provides an overview on the structure and working mechanism of trypsin, followed by a critical analysis of its cleavage behavior, typically simply accepted to occur exclusively yet consistently after Arg and Lys, unless they are followed by a Pro. In this context, shortcomings in our ability to understand and predict the behavior of trypsin will be highlighted, along with the downstream implications. Furthermore, an analysis is carried out on the inherent shortcomings of trypsin with regard to whole proteome analysis, and alternative approaches will be presented that can alleviate these issues. Finally, some reflections on the future of trypsin as the workhorse protease in mass spectrometry-based proteomics will be provided.
Collapse
Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | | | | |
Collapse
|
40
|
Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Schmuth M, Gruber R. Distinguishing ichthyoses by protein profiling. PLoS One 2013; 8:e75355. [PMID: 24130705 PMCID: PMC3793978 DOI: 10.1371/journal.pone.0075355] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/13/2013] [Indexed: 12/22/2022] Open
Abstract
To explore the usefulness of protein profiling for characterization of ichthyoses, we here determined the profile of human epidermal stratum corneum by shotgun proteomics. Samples were analyzed after collection on tape circles from six anatomic sites (forearm, palm, lower leg, forehead, abdomen, upper back), demonstrating site-specific differences in profiles. Additional samples were collected from the forearms of subjects with ichthyosis vulgaris (filaggrin (FLG) deficiency), recessive X-linked ichthyosis (steroid sulfatase (STS) deficiency) and autosomal recessive congenital ichthyosis type lamellar ichthyosis (transglutaminase 1 (TGM1) deficiency). The ichthyosis protein expression patterns were readily distinguishable from each other and from phenotypically normal epidermis. In general, the degree of departure from normal was lower from ichthyosis vulgaris than from lamellar ichthyosis, parallel to the severity of the phenotype. Analysis of samples from families with ichthyosis vulgaris and concomitant modifying gene mutations (STS deficiency, GJB2 deficiency) permitted correlation of alterations in protein profile with more complex genetic constellations.
Collapse
Affiliation(s)
- Robert H. Rice
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, United States of America
| | - Katie M. Bradshaw
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, United States of America
| | - Blythe P. Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California Davis, Davis, California, United States of America
| | - David M. Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core and Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - Richard A. Eigenheer
- Proteomics Core Facility, University of California Davis, Davis, California, United States of America
| | - Brett S. Phinney
- Proteomics Core Facility, University of California Davis, Davis, California, United States of America
| | - Matthias Schmuth
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck, Austria
| | - Robert Gruber
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck, Austria
| |
Collapse
|
41
|
Hu Q, Rice RH, Qin Q, Phinney BS, Eigenheer RA, Bao W, Zhao B. Proteomic analysis of human keratinocyte response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure. J Proteome Res 2013; 12:5340-7. [PMID: 23991859 DOI: 10.1021/pr4006266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chronic exposure to 2,3,7,8-tetrachlorodibeno-p-dioxin (TCDD) and related polyhalogenated organic pollutants occurs as a consequence of modern life. Exploring the cellular basis for their action is anticipated to help understand the risk they pose and improve the foundation for their regulation. A basis for the striking change in human keratinocyte colony morphology due to TCDD exposure has been investigated by shotgun proteomics. Concentrating on changes in protein levels among three cell strains has revealed significant decreases in the differentiation markers filaggrin, keratin 1, and keratin 10. EGF treatment in concert with TCDD enhanced the changes in these markers and several other proteins while reducing the levels of certain other proteins. The only protein stimulated by TCDD in all three strains and reversed by EGF in them was vimentin, not previously observed to be in the aryl hydrocarbon receptor response domain. Although TCDD is often proposed to enhance keratinocyte differentiation, proteomic analysis reveals it uncouples the differentiation program and suggests that reduced levels of differentiation marker proteins contribute to the observed excessive stratification it induces.
Collapse
Affiliation(s)
- Qin Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | | | | | | | | | | | | |
Collapse
|
42
|
Kim JS, Monroe ME, Camp DG, Smith RD, Qian WJ. In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. J Proteome Res 2013; 12:910-6. [PMID: 23268687 DOI: 10.1021/pr300955f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partially tryptic peptides are often identified in shotgun proteomics using trypsin as the proteolytic enzyme; however, their sources have been controversial. Herein, we investigate the impact of in-source fragmentation on shotgun proteomics profiling of three biological samples: a standard protein mixture, a mouse brain tissue homogenate, and mouse plasma. Because the in-source fragments of peptide ions have the same LC elution time as their parental peptides, partially tryptic peptide ions from in-source fragmentation can be distinguished from other partially tryptic peptides based on their elution time differences from those computationally predicted data. The percentage of partially tryptic peptide identifications resulting from in-source fragmentation in a standard protein digest was observed to be ∼60%. In more complex mouse brain or plasma samples, in-source fragmentation contributed to a lesser degree of 1-3% of all identified peptides due to the limited dynamic range of LC-MS/MS measurements. The other major source of partially tryptic peptides in complex biological samples is presumably proteolytic cleavage by endogenous proteases in the samples. Our work also provides a method to identify such proteolytic-derived partially tryptic peptides due to endogenous proteases in the samples by removing in-source fragmentation artifacts from the identified peptides.
Collapse
Affiliation(s)
- Jong-Seo Kim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | | | | | | |
Collapse
|
43
|
Rice RH, Winters BR, Durbin-Johnson BP, Rocke DM. Chicken corneocyte cross-linked proteome. J Proteome Res 2013; 12:771-6. [PMID: 23256538 DOI: 10.1021/pr301036k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Shotgun proteomic analysis was performed of epidermal scale, feather, beak and claw from the domestic chicken. To this end, the samples were separated first into solubilized and particulate fractions, the latter enriched in isopeptide cross-linking, by exhaustive extraction in sodium dodecyl sulfate under reducing conditions. Among the 205 proteins identified were 17 keratins (types α and β), 51 involved in protein synthesis, 8 junctional, 8 histone, 5 heat shock, and 5 14-3-3 proteins. Considerable overlap among the beak, claw, feather, and scale samples was observed in protein profiles, but those from beak and claw were the most similar. Scale and feather profiles were the most distinctive, each exhibiting specific proteins. Less than 20% of the proteins were found only in the detergent-solubilized fraction, while 34-57% were found only in the particulate fraction, depending on the source, and the rest in both fractions. The results provide the first comprehensive analysis of the content of these cornified structures, reveal the efficient use of available proteins in conferring mechanical and chemical stability to them, and emphasize the importance of isopeptide cross-linking in avian epithelial cornification.
Collapse
Affiliation(s)
- Robert H Rice
- Department of Environmental Toxicology, University of California Davis, Davis, California 95616, USA.
| | | | | | | |
Collapse
|
44
|
Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Sundberg JP. Differentiating inbred mouse strains from each other and those with single gene mutations using hair proteomics. PLoS One 2012; 7:e51956. [PMID: 23251662 PMCID: PMC3522583 DOI: 10.1371/journal.pone.0051956] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023] Open
Abstract
Mutant laboratory mice with distinctive hair phenotypes are useful for identifying genes responsible for hair diseases. The work presented here demonstrates that shotgun proteomic profiling can distinguish hair shafts from different inbred mouse strains. For this purpose, analyzing the total hair shaft provided better discrimination than analyzing the isolated solubilized and particulate (cross-linked) fractions. Over 100 proteins exhibited significant differences among the 11 strains and 5 mutant stocks across the wide spectrum of strains surveyed. Effects on the profile of single gene mutations causing hair shaft defects were profound. Since the hair shaft provides a discrete sampling of the species proteome, with constituents serving important functions in epidermal appendages and throughout the body, this work provides a foundation for non-invasive diagnosis of genetic diseases of hair and perhaps other tissues.
Collapse
Affiliation(s)
- Robert H Rice
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, USA.
| | | | | | | | | | | | | |
Collapse
|
45
|
Sun L, Zhu G, Li Y, Yang P, Dovichi NJ. Coupling methanol denaturation, immobilized trypsin digestion, and accurate mass and time tagging for liquid-chromatography-based shotgun proteomics of low nanogram amounts of RAW 264.7 cell lysate. Anal Chem 2012; 84:8715-21. [PMID: 22971241 PMCID: PMC3477608 DOI: 10.1021/ac3019608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the shotgun proteomic analysis of mammalian cell lysates that contain low nanogram amounts of protein. Proteins were denatured using methanol, digested using immobilized trypsin, and analyzed by UPLC-ESI-MS/MS. The approach generated more peptides and higher sequence coverage for a mixture of three standard proteins than the use of free trypsin solution digestion of heat- or urea-denatured proteins. We prepared triplicate RAW 264.7 cell lysates that contained 6, 30, 120, and 300 ng of protein. An average of 2 ± 1, 23 ± 2, 134 ± 11, and 218 ± 26 proteins were detected for each sample size, respectively. The numbers of both protein and peptide IDs scaled linearly with the amount of sample taken for analysis. Our approach also outperformed traditional methods (free trypsin digestion of heat- or urea-denatured proteins) for 6-300 ng RAW 264.7 cell protein analysis in terms of number of peptides and proteins identified. The use of accurate mass and time (AMT) tags resulted in the identification of an additional 16 proteins based on 20 peptides from the 6 ng cell lysate prepared with our approach. When AMT analysis was performed for the 6 ng cell lysate prepared with traditional methods, no reasonable peptide signal could be obtained. In all cases, roughly ∼30% of the digested sample was taken for analysis, corresponding to the analysis of a 2 ng aliquot of homogenate from the 6 ng cell lysate.
Collapse
Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yihan Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ping Yang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
46
|
High throughput profiling of serum phosphoproteins/peptides using the SELDI-TOF-MS platform. Methods Mol Biol 2012; 818:199-216. [PMID: 22083825 DOI: 10.1007/978-1-61779-418-6_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Protein phosphorylation is a dynamic post-translational modification that plays a critical role in the regulation of a wide spectrum of biological events and cellular functions including signal transduction, gene expression, cell proliferation, and apoptosis. Determination of the sites and magnitudes of protein phosphorylation has been an essential step in the analysis of the control of many biological systems. A high throughput analysis of phosphorylation of proteins would provide a simple, logical, and useful tool for a functional dissection and prediction of biological functions and signaling pathways in association with these important molecular events. We have developed a functional proteomics technique using the ProteinChip array-based SELDI-TOF-MS analysis for high throughput profiling of phosphoproteins/phosphopeptides in human serum for the early detection and diagnosis as well as for the molecular staging of human cancer. The methodology and experimental approach consists of five steps: (1) generation of a total peptide pool of serum proteins by a global trypsin digestion; (2) rapid isolation of phosphopeptides from the total serum peptide pool by an affinity selection, purification, and enrichment using a novel automated micro-bioprocessing system with phospho-antibody-conjugated paramagnetic beads and a hybrid magnet plate; (3) high throughput phosphopeptide analysis on ProteinChip arrays by automated SELDI-TOF-MS; and (4) bioinformatics and statistical methods for data analysis. This method with appropriate modifications may be equally applicable to serine-, threonine- and tyrosine-phosphorylated proteins and for selectively isolating, profiling, and identifying phosphopeptides present in a highly complex phosphor-peptide mixture prepared from various human specimens such as cells, tissue samples, and serum and other body fluids.
Collapse
|
47
|
Mata-Gómez MA, Yasui MT, Guerrero-Rangel A, Valdés-Rodríguez S, Winkler R. Accelerated identification of proteins by mass spectrometry by employing covalent pre-gel staining with Uniblue A. PLoS One 2012; 7:e31438. [PMID: 22363648 PMCID: PMC3281962 DOI: 10.1371/journal.pone.0031438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 01/08/2012] [Indexed: 12/21/2022] Open
Abstract
Background The identification of proteins by mass spectrometry is a standard method in biopharmaceutical quality control and biochemical research. Prior to identification by mass spectrometry, proteins are usually pre-separated by electrophoresis. However, current protein staining and de-staining protocols are tedious and time consuming, and therefore prolong the sample preparation time for mass spectrometry. Methodology and Principal Findings We developed a 1-minute covalent pre-gel staining protocol for proteins, which does not require de-staining before the mass spectrometry analysis. We investigated the electrophoretic properties of derivatized proteins and peptides and studied their behavior in mass spectrometry. Further, we elucidated the preferred reaction of proteins with Uniblue A and demonstrate the integration of the peptide derivatization into typical informatics tools. Conclusions and Significance The Uniblue A staining method drastically speeds up the sample preparation for the mass spectrometry based identification of proteins. The application of this chemo-proteomic strategy will be advantageous for routine quality control of proteins and for time-critical tasks in protein analysis.
Collapse
Affiliation(s)
- Marco A. Mata-Gómez
- Department of Biotechnology and Food Engingeering, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Matthew T. Yasui
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, United States of America
| | - Armando Guerrero-Rangel
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Silvia Valdés-Rodríguez
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Robert Winkler
- Department of Biotechnology and Food Engingeering, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Irapuato, Guanajuato, Mexico
- * E-mail:
| |
Collapse
|
48
|
Wang H, Tang HY, Tan GC, Speicher DW. Data analysis strategy for maximizing high-confidence protein identifications in complex proteomes such as human tumor secretomes and human serum. J Proteome Res 2011; 10:4993-5005. [PMID: 21955121 DOI: 10.1021/pr200464c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Detection of biologically interesting, low-abundance proteins in complex proteomes such as serum typically requires extensive fractionation and high-performance mass spectrometers. Processing of the resulting large data sets involves trade-offs between confidence of identification and depth of protein coverage; that is, higher stringency filters preferentially reduce the number of low-abundance proteins identified. In the current study, an alternative database search and results filtering strategies were evaluated using test samples ranging from purified proteins to ovarian tumor secretomes and human serum to maximize peptide and protein coverage. Full and partial tryptic searches were compared because substantial numbers of partial tryptic peptides were observed in all samples, and the proportion of partial tryptic peptides was particularly high for serum. When data filters that yielded similar false discovery rates (FDR) were used, full tryptic searches detected far fewer peptides than partial tryptic searches. In contrast to the common practice of using full tryptic specificity and a narrow precursor mass tolerance, more proteins and peptides could be confidently identified using a partial tryptic database search with a 100 ppm precursor mass tolerance followed by filtering of results using 10 ppm mass error and full tryptic boundaries.
Collapse
Affiliation(s)
- Huan Wang
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | | |
Collapse
|
49
|
Chiu ML, Ytterberg AJ, Ogorzalek Loo RR, Loo JA, Monbouquette HG. Characterization of morphine-glucose-6-phosphate dehydrogenase conjugates by mass spectrometry. Bioconjug Chem 2011; 22:1595-604. [PMID: 21678975 DOI: 10.1021/bc2001352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A key characteristic of the analyte-reporter enzyme conjugate used in the enzyme-multiplied immunoassay technique (EMIT) is the inhibition of the conjugate enzyme upon anti-analyte antibody binding. To improve our understanding of the antibody-induced inhibition mechanism, we characterized morphine-glucose-6-phosphate dehydrogenase (G6PDH) conjugates as model EMIT analyte-reporter enzyme conjugates. Morphine-G6PDH conjugates were prepared by acylating predominantly the primary amines on G6PDH with morphine 3-glucuronide NHS ester molecules. In this study, morphine-G6PDH conjugates were characterized using a combination of methods, including tryptic digestion, immunoprecipitation, matrix-assisted laser desorption ionization mass spectrometry, and electrospray ionization tandem mass spectrometry. Twenty-six conjugation sites were identified. The identified sites all were found to be primary amines. The degree of conjugation was determined to be less than the number of conjugation sites, suggesting heterogeneity within the morphine-G6PDH conjugate population. Two catalytically important residues in the active site (K22 and K183) were among the identified conjugation sites, explaining at least partially the cause of loss of activity due to the coupling reaction.
Collapse
Affiliation(s)
- May L Chiu
- Department of Chemical and Biomolecular Engineering, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095-1592, United States
| | | | | | | | | |
Collapse
|
50
|
Chamrád I, Strouhal O, Řehulka P, Lenobel R, Šebela M. Microscale affinity purification of trypsin reduces background peptides in matrix-assisted laser desorption/ionization mass spectrometry of protein digests. J Proteomics 2011; 74:948-57. [DOI: 10.1016/j.jprot.2011.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 01/26/2011] [Accepted: 02/09/2011] [Indexed: 11/24/2022]
|