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Article ; Online: Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native

Wojtkiewicz, Melinda / Subramanian, Sabarinath Peruvemba / Gundry, Rebekah L

2024 Volume 96, Issue 15, Page(s) 5746–5751

Abstract: Microflow porous graphitized carbon liquid chromatography (PGC-LC) combined with negative mode ionization mass spectrometry (MS) provides high resolution separation and identification of reduced ... ...

Abstract	Microflow porous graphitized carbon liquid chromatography (PGC-LC) combined with negative mode ionization mass spectrometry (MS) provides high resolution separation and identification of reduced native
MeSH term(s)	Carbon/chemistry ; Liquid Chromatography-Mass Spectrometry ; Tandem Mass Spectrometry/methods ; Porosity ; Polysaccharides/chemistry ; Spectrometry, Mass, Electrospray Ionization/methods
Chemical Substances	Carbon (7440-44-0) ; Polysaccharides
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c03649
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Article ; Online: Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface

Berg Luecke, Linda / Mesidor, Roneldine / Littrell, Jack / Carpenter, Morgan / Wojtkiewicz, Melinda / Gundry, Rebekah L

Journal of proteome research

2024

Abstract: Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of ... ...

Abstract	Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface
Language	English
Publishing date	2024-02-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00800
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Article ; Online: The GENTIL Method for Isolation of Human Adult Cardiomyocytes from Cryopreserved Tissue for Proteomic Analyses.

Waknitz, Michelle / Berg Luecke, Linda / Mesidor, Roneldine / Wojtkiewicz, Melinda / Castro, Chase / Gundry, Rebekah L

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2735, Page(s) 145–167

Abstract: Heart failure is a serious clinical and economic health care problem, and its clinical progression is linked to pathological cardiac remodeling. Due to the heterogeneity of heart failure, lack of animal models to accurately represent advanced heart ... ...

Abstract	Heart failure is a serious clinical and economic health care problem, and its clinical progression is linked to pathological cardiac remodeling. Due to the heterogeneity of heart failure, lack of animal models to accurately represent advanced heart failure, and limited access to fresh human cardiac tissue, little is known regarding cell-type-specific mechanisms and context-specific functions of cardiomyocytes during disease development processes. While mass spectrometry has been increasingly applied to unravel changes in the proteome associated with cardiovascular physiology and disease, most studies have used homogenized tissue. Therefore, new studies using isolated cardiomyocytes are necessary to gain a better understanding of the intricate cell-type-specific molecular mechanisms underlying the pathophysiology of heart failure. This chapter describes the GENTIL method, which incorporates recent technological developments in sample handling, for isolation of cardiomyocytes from cryopreserved human cardiac tissues for use in proteomic analyses.
MeSH term(s)	Animals ; Humans ; Adult ; Myocytes, Cardiac/pathology ; Proteomics/methods ; Heart Failure/pathology ; Mass Spectrometry ; Proteome
Chemical Substances	Proteome
Language	English
Publishing date	2023-12-01
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3527-8_9
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Article ; Online: Facile Preparation of Peptides for Mass Spectrometry Analysis in Bottom-Up Proteomics Workflows.

Wojtkiewicz, Melinda / Berg Luecke, Linda / Kelly, Maia I / Gundry, Rebekah L

Current protocols

2021 Volume 1, Issue 3, Page(s) e85

Abstract: Mass spectrometry (MS) is routinely used to identify, characterize, and quantify biological molecules. For protein analysis, MS-based workflows can be broadly categorized as top-down or bottom-up, depending on whether the proteins are analyzed as intact ... ...

Abstract	Mass spectrometry (MS) is routinely used to identify, characterize, and quantify biological molecules. For protein analysis, MS-based workflows can be broadly categorized as top-down or bottom-up, depending on whether the proteins are analyzed as intact molecules or first digested into peptides. This article outlines steps for preparing peptide samples for MS as part of a bottom-up proteomics workflow, providing versatile methods suitable for discovery and targeted analyses in qualitative and quantitative workflows. Resulting samples contain peptides of suitable size for analysis by MS instrumentation generally available to modern research laboratories, including MS coupled to either liquid chromatography (LC) or matrix-assisted laser desorption/ionization (MALDI) interfaces. This article incorporates recent developments in methodologies and consumables to facilitate sample preparation. The protocols are well-suited to users without prior experience in proteomics and include methods for universally applicable suspension trap processing and for alternate in-solution processing to accommodate a range of sample types. Cleanup, quantification, and fractionation procedures are also described. © 2021 The Authors. Basic Protocol: Preparation of high-complexity peptide samples for mass spectrometry analysis using S-Trap™ processing Alternate Protocol 1: Preparation of low- to moderate-complexity peptide samples for mass spectrometry analysis using in-solution processing Alternate Protocol 2: Detergent, polymer, and salt removal from peptide samples before mass spectrometry analysis using SP2 processing Support Protocol 1: Protein quantification using Pierce 660 nm assay Support Protocol 2: Peptide quantification using Pierce quantitative fluorometric peptide assay Support Protocol 3: High-pH fractionation of complex peptide samples.
MeSH term(s)	Chromatography, Liquid ; Peptides ; Proteomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Workflow
Chemical Substances	Peptides
Language	English
Publishing date	2021-03-22
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.85
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Article ; Online: Bottom-up proteomic analysis of human adult cardiac tissue and isolated cardiomyocytes.

Wojtkiewicz, Melinda / Berg Luecke, Linda / Castro, Chase / Burkovetskaya, Maria / Mesidor, Roneldine / Gundry, Rebekah L

Journal of molecular and cellular cardiology

2021 Volume 162, Page(s) 20–31

Abstract: The heart is composed of multiple cell types, each with a specific function. Cell-type-specific approaches are necessary for defining the intricate molecular mechanisms underlying cardiac development, homeostasis, and pathology. While single-cell RNA-seq ...

Abstract	The heart is composed of multiple cell types, each with a specific function. Cell-type-specific approaches are necessary for defining the intricate molecular mechanisms underlying cardiac development, homeostasis, and pathology. While single-cell RNA-seq studies are beginning to define the chamber-specific cellular composition of the heart, our views of the proteome are more limited because most proteomics studies have utilized homogenized human cardiac tissue. To promote future cell-type specific analyses of the human heart, we describe the first method for cardiomyocyte isolation from cryopreserved human cardiac tissue followed by flow cytometry for purity assessment. We also describe a facile method for preparing isolated cardiomyocytes and whole cardiac tissue homogenate for bottom-up proteomic analyses. Prior experience in dissociating cardiac tissue or proteomics is not required to execute these methods. We compare different sample preparation workflows and analysis methods to demonstrate how these can impact the depth of proteome coverage achieved. We expect this how-to guide will serve as a starting point for investigators interested in general and cell-type-specific views of the cardiac proteome.
MeSH term(s)	Humans ; Myocytes, Cardiac/metabolism ; Proteome/metabolism ; Proteomics/methods ; Specimen Handling
Chemical Substances	Proteome
Language	English
Publishing date	2021-08-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80157-4
ISSN	1095-8584 ; 0022-2828
ISSN (online)	1095-8584
ISSN	0022-2828
DOI	10.1016/j.yjmcc.2021.08.008
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Zs.A 426: Show issues

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Article ; Online: Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts.

Luecke, Linda Berg / Waas, Matthew / Littrell, Jack / Wojtkiewicz, Melinda / Castro, Chase / Burkovetskaya, Maria / Schuette, Erin N / Buchberger, Amanda Rae / Churko, Jared M / Chalise, Upendra / Waknitz, Michelle / Konfrst, Shelby / Teuben, Roald / Morrissette-McAlmon, Justin / Mahr, Claudius / Anderson, Daniel R / Boheler, Kenneth R / Gundry, Rebekah L

Nature cardiovascular research

2023 Volume 2, Issue 1, Page(s) 76–95

Abstract: Cardiac cell surface proteins are drug targets and useful biomarkers for discriminating among cellular phenotypes and disease states. Here we developed an analytical platform, CellSurfer, that enables quantitative cell surface proteome (surfaceome) ... ...

Abstract	Cardiac cell surface proteins are drug targets and useful biomarkers for discriminating among cellular phenotypes and disease states. Here we developed an analytical platform, CellSurfer, that enables quantitative cell surface proteome (surfaceome) profiling of cells present in limited quantities, and we apply it to isolated primary human heart cells. We report experimental evidence of surface localization and extracellular domains for 1,144
Language	English
Publishing date	2023-01-16
Publishing country	England
Document type	Journal Article
ISSN	2731-0590
ISSN (online)	2731-0590
DOI	10.1038/s44161-022-00200-y
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Article ; Online: Two methods for proteomic analysis of formalin-fixed, paraffin embedded tissue result in differential protein identification, data quality, and cost.

Luebker, Stephen A / Wojtkiewicz, Melinda / Koepsell, Scott A

Proteomics

2015 Volume 15, Issue 21, Page(s) 3744–3753

Abstract: Formalin-fixed paraffin-embedded (FFPE) tissue is a rich source of clinically relevant material that can yield important translational biomarker discovery using proteomic analysis. Protocols for analyzing FFPE tissue by LC-MS/MS exist, but ... ...

Abstract	Formalin-fixed paraffin-embedded (FFPE) tissue is a rich source of clinically relevant material that can yield important translational biomarker discovery using proteomic analysis. Protocols for analyzing FFPE tissue by LC-MS/MS exist, but standardization of procedures and critical analysis of data quality is limited. This study compared and characterized data obtained from FFPE tissue using two methods: a urea in-solution digestion method (UISD) versus a commercially available Qproteome FFPE Tissue Kit method (Qkit). Each method was performed independently three times on serial sections of homogenous FFPE tissue to minimize pre-analytical variations and analyzed with three technical replicates by LC-MS/MS. Data were evaluated for reproducibility and physiochemical distribution, which highlighted differences in the ability of each method to identify proteins of different molecular weights and isoelectric points. Each method replicate resulted in a significant number of new protein identifications, and both methods identified significantly more proteins using three technical replicates as compared to only two. UISD was cheaper, required less time, and introduced significant protein modifications as compared to the Qkit method, which provided more precise and higher protein yields. These data highlight significant variability among method replicates and type of method used, despite minimizing pre-analytical variability. Utilization of only one method or too few replicates (both method and technical) may limit the subset of proteomic information obtained.
MeSH term(s)	Chromatography, Liquid/economics ; Chromatography, Liquid/methods ; Data Accuracy ; Formaldehyde/chemistry ; Humans ; Isoelectric Point ; Paraffin Embedding ; Peptides/analysis ; Peptides/isolation & purification ; Proteome/analysis ; Proteome/isolation & purification ; Proteomics/economics ; Proteomics/methods ; Tandem Mass Spectrometry/economics ; Tandem Mass Spectrometry/methods ; Tissue Fixation
Chemical Substances	Peptides ; Proteome ; Formaldehyde (1HG84L3525)
Language	English
Publishing date	2015-11
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201500147
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Safety, tolerability, and immune-biomarker profiling for year-long sargramostim treatment of Parkinson's disease.

Olson, Katherine E / Namminga, Krista L / Lu, Yaman / Schwab, Aaron D / Thurston, Mackenzie J / Abdelmoaty, Mai M / Kumar, Vikas / Wojtkiewicz, Melinda / Obaro, Helen / Santamaria, Pamela / Mosley, R Lee / Gendelman, Howard E

EBioMedicine

2021 Volume 67, Page(s) 103380

Abstract: Background: Neuroinflammation plays a pathogenic role in Parkinson's disease (PD). Immunotherapies that restore brain homeostasis can mitigate neurodegeneration by transforming T cell phenotypes. Sargramostim has gained considerable attention as an ... ...

Abstract	Background: Neuroinflammation plays a pathogenic role in Parkinson's disease (PD). Immunotherapies that restore brain homeostasis can mitigate neurodegeneration by transforming T cell phenotypes. Sargramostim has gained considerable attention as an immune transformer through laboratory bench to bedside clinical studies. However, its therapeutic use has been offset by dose-dependent adverse events. Therefore, we performed a reduced drug dose regimen to evaluate safety and to uncover novel disease-linked biomarkers during 5 days/week sargramostim treatments for one year. Methods: Five PD subjects were enrolled in a Phase 1b, unblinded, open-label study to assess safety and tolerability of 3 μg/kg/day sargramostim. Complete blood counts and chemistry profiles, physical examinations, adverse events (AEs), immune profiling, Movement Disorder Society-Sponsored Revision of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS) scores, T cell phenotypes/function, DNA methylation, and gene and protein patterns were evaluated. Findings: Sargramostim administered at 3 μg/kg/day significantly reduced numbers and severity of AEs/subject/month compared to 6 μg/kg/day treatment. While MDS-UPDRS Part III score reductions were recorded, peripheral blood immunoregulatory phenotypes and function were elevated. Hypomethylation of upstream FOXP3 DNA elements was also increased. Interpretation: Long-term sargramostim treatment at 3 μg/kg/day is well-tolerated and effective in restoring immune homeostasis. There were decreased numbers and severity of AEs and restored peripheral immune function coordinate with increased numbers and function of Treg. MDS-UPDRS Part III scores did not worsen. Larger patient numbers need be evaluated to assess conclusive drug efficacy (ClinicalTrials.gov NCT03790670). Funding: The research was supported by community funds to the University of Nebraska Foundation and federal research support from 5 R01NS034239-25.
MeSH term(s)	Aged ; Antiparkinson Agents/administration & dosage ; Antiparkinson Agents/adverse effects ; Antiparkinson Agents/therapeutic use ; Biomarkers/analysis ; Granulocyte-Macrophage Colony-Stimulating Factor/administration & dosage ; Granulocyte-Macrophage Colony-Stimulating Factor/adverse effects ; Granulocyte-Macrophage Colony-Stimulating Factor/therapeutic use ; Humans ; Male ; Middle Aged ; Parkinson Disease/drug therapy ; Parkinson Disease/immunology ; Recombinant Proteins/administration & dosage ; Recombinant Proteins/adverse effects ; Recombinant Proteins/therapeutic use ; T-Lymphocytes/immunology
Chemical Substances	Antiparkinson Agents ; Biomarkers ; Recombinant Proteins ; sargramostim (5TAA004E22) ; Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1)
Language	English
Publishing date	2021-05-14
Publishing country	Netherlands
Document type	Clinical Trial, Phase I ; Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2021.103380
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Article ; Online: The effects of maturation and aging on the rotator cuff tendon-to-bone interface.

Jiang, Xiping / Wojtkiewicz, Melinda / Patwardhan, Chinmay / Greer, Sydney / Kong, Yunfan / Kuss, Mitchell / Huang, Xi / Liao, Jun / Lu, Yongfeng / Dudley, Andrew / Gundry, Rebekah L / Fuchs, Matthias / Streubel, Philipp / Duan, Bin

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2021 Volume 35, Issue 12, Page(s) e22066

Abstract: Rotator cuff tendon injuries often occur at the tendon-to-bone interface (i.e., enthesis) area, with a high prevalence for the elderly population, but the underlying reason for this phenomenon is still unknown. The objective of this study is to identify ... ...

Abstract	Rotator cuff tendon injuries often occur at the tendon-to-bone interface (i.e., enthesis) area, with a high prevalence for the elderly population, but the underlying reason for this phenomenon is still unknown. The objective of this study is to identify the histological, molecular, and biomechanical alterations of the rotator cuff enthesis with maturation and aging in a mouse model. Four different age groups of mice (newborn, young, adult, and old) were studied. Striking variations of the entheses were observed between the newborn and other matured groups, with collagen content, proteoglycan deposition, collagen fiber dispersion was significantly higher in the newborn group. The compositional and histological features of young, adult, and old groups did not show significant differences, except having increased proteoglycan deposition and thinner collagen fibers at the insertion sites in the old group. Nanoindentation testing showed that the old group had a smaller compressive modulus at the insertion site when compared with other groups. However, tensile mechanical testing reported that the old group demonstrated a significantly higher failure stress when compared with the young and adult groups. The proteomics analysis detected dramatic differences in protein content between newborn and young groups but minor changes among young, adult, and old groups. These results demonstrated: (1) the significant alterations of the enthesis composition and structure occur from the newborn to the young time period; (2) the increased risk of rotator cuff tendon injuries in the elderly population is not solely because of old age alone in the rodent model.
MeSH term(s)	Age Factors ; Aging ; Animals ; Biomechanical Phenomena ; Bone and Bones/metabolism ; Bone and Bones/pathology ; Collagen/metabolism ; Disease Models, Animal ; Mice ; Proteoglycans/metabolism ; Proteome/metabolism ; Rotator Cuff/metabolism ; Rotator Cuff/pathology ; Rotator Cuff Injuries/etiology ; Rotator Cuff Injuries/metabolism ; Rotator Cuff Injuries/pathology ; Tendons/metabolism ; Tendons/pathology ; Wound Healing
Chemical Substances	Proteoglycans ; Proteome ; Collagen (9007-34-5)
Language	English
Publishing date	2021-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.202101484R
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Article ; Online: Proteomic profiling of HIV-infected T-cells by SWATH mass spectrometry.

DeBoer, Jason / Wojtkiewicz, Melinda S / Haverland, Nicole / Li, Yan / Harwood, Emma / Leshen, Emily / George, Joseph W / Ciborowski, Pawel / Belshan, Michael

Virology

2018 Volume 516, Page(s) 246–257

Abstract: Viral pathogenesis results from changes in host cells due to virus usurpation of the host cell and the innate cellular responses to thwart infection. We measured global changes in protein expression and localization in HIV-1 infected T-cells using ... ...

Abstract	Viral pathogenesis results from changes in host cells due to virus usurpation of the host cell and the innate cellular responses to thwart infection. We measured global changes in protein expression and localization in HIV-1 infected T-cells using subcellular fractionation and the Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) proteomic platform. Eight biological replicates were performed in two independent experimental series. In silico merging of both experiments identified 287 proteins with altered expression (p < .05) between control and infected cells- 172 in the cytoplasm, 84 in the membrane, and 31 in nuclei. 170 of the proteins are components of the NIH HIV interaction database. Multiple Reaction Monitoring and traditional immunoblotting validated the altered expression of several factors during infection. Numerous factors were found to affect HIV infection in gain- and loss-of-expression infection assays, including the intermediate filament vimentin which was found to be required for efficient infection.
MeSH term(s)	HIV Infections/genetics ; HIV Infections/metabolism ; HIV Infections/virology ; HIV-1/physiology ; Humans ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism ; Proteomics ; T-Lymphocytes/chemistry ; T-Lymphocytes/metabolism ; T-Lymphocytes/virology ; Tandem Mass Spectrometry
Chemical Substances	Proteins
Language	English
Publishing date	2018-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2018.01.025
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