Peter Hoffmann

University of South Australia

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Manuela Klingler‐Hoffmann

University of South Australia

Martin K. Oehler

University of Adelaide

Mark R. Condina

University of South Australia

Matthew T. Briggs

University of South Australia

Shaun R. McColl

University of Adelaide

Parul Mittal

University of South Australia

Clifford Young

University of South Australia

Ove Gustafsson

University of Melbourne

Gurjeet Kaur

Punjabi University

Georgia Arentz

University of Adelaide

Cooperative Institutions

University of Adelaide

225

University of South Australia

108

University of Melbourne

South Australia Pathology

Centre for Cancer Biology

Royal Adelaide Hospital

Macquarie University

Monash University

Medizinische Hochschule Hannover

Hanson Institute

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Quantitative analysis of the spinal cord CD4+T lymphocyte proteome in EAE

Multiple Sclerosis Journal (2012)

Shaun R. McColl Michelle E. Turvey Tomas Koudelka William M. Carroll Claude C.A. Bernard

Proteome

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Citations (0)

Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis

APOPTOSIS (2013)

Ibrahim O. Alanazi Esmaeil Ebrahimie Peter Hoffmann David L. Adelson

A431 cells

FADD

Intrinsic apoptosis

10.1007/s10495-013-0887-6

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Citations (25)

Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215: A non two-dimensional gel electrophoresis-based proteome analysis strategy

PROTEOMICS (2001)

Peter Hoffmann Hong Ji Robert L. Moritz Lisa Connolly David F. Frecklington

The conventional approach for analyzing the protein complement of a genome involves the combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometric based protein identification technologies. While 2-DE is a powerful separation technique, it is severely limited by the insolubility of certain classes of proteins (e.g. hydrophobic membrane proteins), as well as the amount of protein that can be processed. Here, we describe a simple procedure for resolving complex mixtures of proteins that involves a combination of free flow electrophoresis (FFE), a liquid-based isoelectric focussing (IEF) method, and sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Resolved proteins were identified by peptide fragment sequencing using capillary column reversed-phase high performance liquid chromatography (RP-HPLC)/mass spectrometry (MS). An initial demonstration of the method was performed using digitonin/ethylenediaminetetraacetic acid EDTA extracted cytosolic proteins from the human colon carcinoma cell line, LIM 1215. Cytosolic proteins were separated by liquid-based IEF (pH range 3-10) into 96 fractions, and each FFE fraction was further fractionated by SDS-PAGE. Selected protein bands were excised from the SDS-PAGE gel, digested in situ with trypsin, and subsequently identified by on-line RP-HPLC/electrospray-ionization ion trap MS. Our results indicate that FFE is: (i) an extremely powerful liquid-based IEF method for resolving proteins; (ii) not limited by the amount of sample that can be loaded onto the instrument; and (iii) capable of fractionating intact protein complexes (a potentially powerful tool for cell-mapping proteomics). An up-to-date list of cytosolic proteins from the human colorectal carcinoma cell line LIM 1215 can be found in the Joint Protein Structure Laboratory (JPSL) proteome database. This information will provide an invaluable resource for future proteomics-based biological studies of colon cancer. The JPSL proteome database can be accessed through the World Wide Web (WWW) network (http://www.ludwig.edu.au/jpsl/jpslhome.html).

Free-flow electrophoresis

Proteome

Bottom-up proteomics

Peptide mass fingerprinting

10.1002/1615-9861(200107)1:7<807::aid-prot807>3.0.co;2-6

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Citations (123)

A Combined Free Flow Electrophoresis and DIGE Approach to Compare Proteins in Complex Biological Samples

Methods in molecular biology (2012)

Kim Y. C. Fung Chris Cursaro Tanya Lewanowitsch Leah Cosgrove Peter Hoffmann

Free-flow electrophoresis

Difference gel electrophoresis

Label-free Quantification

10.1007/978-1-61779-821-4_12

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Citations (1)

Label-Free Quantification Mass Spectrometry Identifies Protein Markers of Chemotherapy Response in High-Grade Serous Ovarian Cancer

Cancers (2023)

Georgia Arentz Parul Mittal Manuela Klingler‐Hoffmann Mark R. Condina Carmela Ricciardelli

Eighty percent of ovarian cancer patients initially respond to chemotherapy, but the majority eventually experience a relapse and die from the disease with acquired chemoresistance. In addition, 20% of patients do not respond to treatment at all, as their disease is intrinsically chemotherapy resistant. Data-independent acquisition nano-flow liquid chromatography-mass spectrometry (DIA LC-MS) identified the three protein markers: gelsolin (GSN), calmodulin (CALM1), and thioredoxin (TXN), to be elevated in high-grade serous ovarian cancer (HGSOC) tissues from patients that responded to chemotherapy compared to those who did not; the differential expression of the three protein markers was confirmed by immunohistochemistry. Analysis of the online GENT2 database showed that mRNA levels of GSN, CALM1, and TXN were decreased in HGSOC compared to fallopian tube epithelium. Elevated levels of GSN and TXN mRNA expression correlated with increased overall and progression-free survival, respectively, in a Kaplan-Meier analysis of a large online repository of HGSOC patient data. Importantly, differential expression of the three protein markers was further confirmed when comparing parental OVCAR-5 cells to carboplatin-resistant OVCAR-5 cells using DIA LC-MS analysis. Our findings suggest that GSN, CALM1, and TXN may be useful biomarkers for predicting chemotherapy response and understanding the mechanisms of chemotherapy resistance. Proteomic data are available via ProteomeXchange with identifier PXD033785.

Carboplatin

10.3390/cancers15072172

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Citations (4)

Microbiological quality of grated cheeses of different commercial brands obtained at various markets in the municipality of Sao Jose do Rio Preto, SP

Higiene Alimentar/Higiene alimentar (2004)

Fernando Leite Hoffmann Tânia Gonçalves Anabela Coelho Elisa Yoko Hirooka Peter Hoffmann

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Optimal preparation methods for automated matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry profiling of low molecular weight proteins and peptides

Rapid Communications in Mass Spectrometry (2009)

Megan A. S. Penno Matthias Ernst Peter Hoffmann

Abstract Mass spectrometry (MS) profiling of the proteome and peptidome for disease‐associated patterns is a new concept in clinical diagnostics. The technique, however, is highly sensitive to external sources of variation leading to potentially unacceptable numbers of false positive and false negative results. Before MS profiling can be confidently implemented in a medical setting, standard experimental methods must be developed that minimize technical variance. Past studies of variance have focused largely on pre‐analytical variation (i.e., sample collection, handling, etc.). Here, we examined how factors at the analytical stage including the matrix and solid‐phase extraction influence MS profiling. Firstly, a standard peptide/protein sample was measured automatically by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) MS across five consecutive days using two different preparation methods, dried droplet and sample/matrix, of four types of matrix: α ‐cyano‐4‐hydroxycinnamic acid (HCCA), sinapinic acid (SA), 2,5‐dihydroxybenzoic acid (DHB) and 2,5‐dihydroxyacetophenone (DHAP). The results indicated that the matrix preparation greatly influenced a number of key parameters of the spectra including repeatability (within‐day variability), reproducibility (inter‐day variability), resolution, signal strength, background intensity and detectability. Secondly, an investigation into the variance associated with C8 magnetic bead extraction of the standard sample prior to automated MS profiling demonstrated that the process did not adversely affect these same parameters. In fact, the spectra were generally more robust following extraction. Thirdly, the best performing matrix preparations were evaluated using C8 magnetic bead extracted human plasma. We conclude that the DHAP prepared according to the dried‐droplet method is the most appropriate matrix to use when performing automated MS profiling. Copyright © 2009 John Wiley & Sons, Ltd.

Sample Preparation

Repeatability

Surface-enhanced laser desorption/ionization

Matrix (chemical analysis)

10.1002/rcm.4167

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Citations (27)

Stauffenberg, Claus Schenk Graf von

Religion Past and Present (2014)

Peter Hoffmann

10.1163/1877-5888_rpp_sim_025730

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Citations (0)

N‐ Glycan matrix‐assisted laser desorption/ionization mass spectrometry imaging protocol for formalin‐fixed paraffin‐embedded tissues

Rapid Communications in Mass Spectrometry (2017)

Matthew T. Briggs Yin Ying Ho Gurjeet Kaur Martin K. Oehler Arun Everest‐Dass

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) of the proteome of a tissue has been an established technique for the past decade. In the last few years, MALDI-MSI of the N-glycome has emerged as a novel MALDI-MSI technique. To assess the accuracy and clinical significance of the N-linked glycan spatial distribution, we have developed a method that utilises MALDI-MSI followed by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) in order to assign glycan structures to the differentiating MALDI-MSI glycan masses released from the tissue glycoproteins.Our workflow presents a comprehensive list of instructions on how to (i) apply MALDI-MSI to spatially map the N-glycome across formalin-fixed paraffin-embedded (FFPE) clinical samples, (ii) structurally characterise N-glycans extracted from consecutive FFPE tissue sections by LC/MS/MS, and (iii) match relevant N-glycan masses from MALDI-MSI with confirmed N-glycan structures determined by LC/MS/MS.Our protocol provides groups that are new to this technique with instructions how to establish N-glycan MALDI-MSI in their laboratory. Furthermore, the method assigns N-glycan structural detail to the masses obtained in the MALDI-MS image. Copyright © 2017 John Wiley & Sons, Ltd.

Mass spectrometry imaging

Matrix (chemical analysis)

10.1002/rcm.7845

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Citations (25)

Multiplexing of radiative-surface plasmon resonance for the detection of gastric cancer biomarkers in a single optical fiber

Sensors and Actuators B Chemical (2013)

Beniamino Sciacca F. Alexandre Peter Hoffmann Tanya M. Monro

10.1016/j.snb.2013.03.131

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Citations (48)