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Articles

The octadecanoids: an emerging class of lipid mediators

Alessandro Quaranta, Johanna Revol-Cavalier, Craig E. Wheelock

Biochem Soc Trans (2022) 50 (6): 1569–1582.

https://doi.org/10.1042/BST20210644

Published: 01 December 2022

... linoleic acid lipid mediators mass spectrometry octadecanoid Oxylipins are broadly defined as enzymatic metabolites of mono- or polyunsaturated fatty acids (PUFAs) produced by at least one step of mono- or dioxygenase-catalyzed oxygenation as well as non-enzymatic products [ 1 ]. These lipids...

View article titled, The octadecanoids: an emerging class of lipid mediators

Articles

LILBID-MS: using lasers to shed light on biomolecular architectures

Nils Hellwig, Janosch Martin, Nina Morgner

Biochem Soc Trans (2022) 50 (3): 1057–1067.

https://doi.org/10.1042/BST20190881

Published: 13 June 2022

... for the analytical tools used to investigate these systems of increased size and complexity, such as Native Mass Spectrometry, which has always been an important tool for structural biology. Scientific advance and recent developments, such as new ways to mimic a cell membrane for a membrane protein, have caused...

View article titled, LILBID-MS: using lasers to shed light on biomolecular architectures

Articles

Norovirus–glycan interactions — how strong are they really?

Thomas Peters, Robert Creutznacher, Thorben Maass, Alvaro Mallagaray, Patrick Ogrissek, Stefan Taube, Lars Thiede, Charlotte Uetrecht

Biochem Soc Trans (2022) 50 (1): 347–359.

https://doi.org/10.1042/BST20210526

Published: 23 December 2021

... structures of VP1 protruding domain dimers, so called P-dimers, complexed with different HBGAs have been solved to atomic resolution. Corresponding binding affinities have been determined for HBGAs and other glycans exploiting different biophysical techniques, with mass spectrometry (MS) and nuclear magnetic...

View article titled, Norovirus–glycan interactions — how strong are they really?

Articles

Chemical biology approaches to study histone interactors

Antony J. Burton, Ghaith M. Hamza, Andrew X. Zhang, Tom W. Muir

Biochem Soc Trans (2021) 49 (5): 2431–2441.

https://doi.org/10.1042/BST20210772

Published: 28 October 2021

... interactors. Recent advances in mapping direct interactors of histone PTMs as well as local chromatin interactomes will be highlighted, with a focus on mass-spectrometry based workflows that continue to illuminate histone-mediated PPIs in unprecedented detail. Protein–protein interactions (PPIs) regulate...

View article titled, Chemical biology approaches to study histone interactors

Articles

The Hitchhiker's guide to glycoproteomics

Tiago Oliveira, Morten Thaysen-Andersen, Nicolle H. Packer, Daniel Kolarich

Biochem Soc Trans (2021) 49 (4): 1643–1662.

https://doi.org/10.1042/BST20200879

Published: 20 July 2021

... glycoproteomics mass spectrometry multi-omics proteomics Protein post-translational modifications (PTMs) enable the cell to produce profound structural and functional diversity from a limited number of protein-encoding genes [ 1 ]. Glycosylation plays an essential role across all domains of life [ 2...

View article titled, The Hitchhiker's guide to glycoproteomics

Articles

Methodology to detect oxidised phospholipids and their relevance in disease

Ahilanandan Dushianthan, Anthony Postle

Biochem Soc Trans (2021) 49 (3): 1241–1250.

https://doi.org/10.1042/BST20200852

Published: 07 May 2021

... have been characterised in detail by a range of mass spectrometry techniques, including direct infusion and liquid chromatography mass spectrometry, there are relatively few reports of comprehensive analyses of oxidised phospholipids in disease states. Oxidised phospholipid species are widely thought...

View article titled, Methodology to detect oxidised phospholipids and their relevance in disease

Articles

A mass spectrometry-based glycotope-centric cellular glycomics is the more fruitful way forward to see the forest for the trees

Kay-Hooi Khoo

Biochem Soc Trans (2021) 49 (1): 55–69.

https://doi.org/10.1042/BST20190861

Published: 25 January 2021

...Kay-Hooi Khoo The nature of protein glycosylation renders cellular glycomics a very challenging task in having to deal with all the disparate glycans carried on membrane glycoproteins. Rapid mapping by mass spectrometry analysis provides only a coarse sketch of the glycomic complexity based...

View article titled, A mass spectrometry-based glycotope-centric cellular glycomics is the more fruitful way forward to see the forest for the trees

Articles

Towards structure-focused glycoproteomics

Anastasia Chernykh, Rebeca Kawahara, Morten Thaysen-Andersen

Biochem Soc Trans (2021) 49 (1): 161–186.

https://doi.org/10.1042/BST20200222

Published: 13 January 2021

...Anastasia Chernykh; Rebeca Kawahara; Morten Thaysen-Andersen Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While...

View article titled, Towards structure-focused glycoproteomics

Articles

Developments in tandem ion mobility mass spectrometry

Charles Eldrid, Konstantinos Thalassinos

Biochem Soc Trans (2020) 48 (6): 2457–2466.

https://doi.org/10.1042/BST20190788

Published: 18 December 2020

...Charles Eldrid; Konstantinos Thalassinos Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments which...

View article titled, Developments in tandem ion mobility mass spectrometry

Articles

Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications

Lindsay K. Pino, Jacob Rose, Amy O'Broin, Samah Shah, Birgit Schilling

Biochem Soc Trans (2020) 48 (5): 1953–1966.

https://doi.org/10.1042/BST20191091

Published: 20 October 2020

...Lindsay K. Pino; Jacob Rose; Amy O'Broin; Samah Shah; Birgit Schilling Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based...

View article titled, Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications

Articles

Mass spectrometry-based methods for structural biology on a proteome-wide scale

Lisa M. Jones

Biochem Soc Trans (2020) 48 (3): 945–954.

https://doi.org/10.1042/BST20190794

Published: 15 May 2020

...Lisa M. Jones Mass spectrometry (MS) has long been used to study proteins mainly via sequence identification and quantitation of expression abundance. In recent years, MS has emerged as a tool for structural biology. Intact protein structural analysis has been enabled by the development of methods...

View article titled, Mass spectrometry-based methods for structural biology on a proteome-wide scale

Articles

In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates

Oliver J. Hale, Helen J. Cooper

Biochem Soc Trans (2020) 48 (1): 317–326.

https://doi.org/10.1042/BST20190793

Published: 03 February 2020

... analysis, desorption electrospray ionisation and nanospray desorption electrospray ionisation. Similarly, developments in native mass spectrometry allow protein–protein and protein–ligand complexes to be ionised and analysed. Identification and characterisation of these large ions involves a suite...

View article titled, In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates

Articles

Structural mass spectrometry comes of age: new insight into protein structure, function and interactions

In Collection

Protein structure and function

Timothy M. Allison, Cherine Bechara

Biochem Soc Trans (2019) 47 (1): 317–327.

https://doi.org/10.1042/BST20180356

Published: 15 January 2019

...Timothy M. Allison; Cherine Bechara Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field...

View article titled, Structural mass spectrometry comes of age: new insight into protein structure, function and interactions

Articles

Mass spectrometry techniques for studying the ubiquitin system

Rachel E. Heap, Megan S. Gant, Frederic Lamoliatte, Julien Peltier, Matthias Trost

Biochem Soc Trans (2017) 45 (5): 1137–1148.

https://doi.org/10.1042/BST20170091

Published: 22 September 2017

..., autoimmunity and neurodegeneration, demonstrating the importance of ubiquitylation. Therefore, enzymes of the ubiquitin system are considered highly attractive drug targets. In recent years, mass spectrometry (MS)-based techniques have become increasingly important in the deciphering of the ubiquitin system...

View article titled, Mass spectrometry techniques for studying the ubiquitin system

Articles

From molecular chaperones to membrane motors: through the lens of a mass spectrometrist

Carol V. Robinson

Biochem Soc Trans (2017) 45 (1): 251–260.

https://doi.org/10.1042/BST20160395

Published: 15 February 2017

... and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made. Moreover...

View article titled, From molecular chaperones to membrane motors: through the lens of a mass spectrometrist

Articles

Oxidative footprinting in the study of structure and function of membrane proteins: current state and perspectives

Vassiliy N. Bavro, Sayan Gupta, Corie Ralston

Biochem Soc Trans (2015) 43 (5): 983–994.

https://doi.org/10.1042/BST20150130

Published: 09 October 2015

... with mass spectrometry (MS) (XF–MS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both low- and high-resolution data from other structural biology approaches, it is capable of providing valuable insights into dynamics of membrane proteins, which...

View article titled, Oxidative footprinting in the study of structure and function of membrane proteins: current state and perspectives

Articles

The role of proteomics in studies of protein moonlighting

Robert J. Beynon, Dean Hammond, Victoria Harman, Yvonne Woolerton

Biochem Soc Trans (2014) 42 (6): 1698–1703.

https://doi.org/10.1042/BST20140277

Published: 17 November 2014

... will require novel analytical and quantitative approaches. 1 To whom correspondence should be addressed (email r.beynon@liv.ac.uk ). 13 10 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 bottom-up mass spectrometry protein moonlighting proteomics...

View article titled, The role of proteomics in studies of protein moonlighting

Articles

Approaches for measuring signalling plasticity in the context of resistance to targeted cancer therapies

Edmund H. Wilkes, Pedro Casado, Pedro R. Cutillas

Biochem Soc Trans (2014) 42 (4): 791–797.

https://doi.org/10.1042/BST20140029

Published: 11 August 2014

... for Activiomics Ltd. 2 To whom correspondence should be addressed (email p.cutillas@qmul.ac.uk ). 21 1 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 acquired resistance cancer mass spectrometry phosphoproteomics signalling plasticity systems biology...

View article titled, Approaches for measuring signalling plasticity in the context of resistance to targeted cancer therapies

Articles

Methods for measuring CoA and CoA derivatives in biological samples

Yugo Tsuchiya, Uyen Pham, Ivan Gout

Biochem Soc Trans (2014) 42 (4): 1107–1111.

https://doi.org/10.1042/BST20140123

Published: 11 August 2014

... 2014 coenzyme A enzymatic assay HPLC mass spectrometry unesterified coenzyme A (CoASH) Since the discovery of CoA (coenzyme A) by Fritz Lipmann over 60 years ago, various methods have been developed to isolate and measure CoA and its thioester derivatives to study their biological...

View article titled, Methods for measuring CoA and CoA derivatives in biological samples

Articles

The complexity of protein semiochemistry in mammals

Robert J. Beynon, Stuart D. Armstrong, Guadalupe Gómez-Baena, Victoria Lee, Deborah Simpson, Jennifer Unsworth, Jane L. Hurst

Biochem Soc Trans (2014) 42 (4): 837–845.

https://doi.org/10.1042/BST20140133

Published: 11 August 2014

... by careful attention to the analytical workflow. 1 To whom correspondence should be addressed (email r.beynon@liv.ac.uk ). 12 5 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 major urinary protein (MUP) mass spectrometry stable isotope QconCAT...

View article titled, The complexity of protein semiochemistry in mammals

Articles

Methylglyoxal in diabetes: link to treatment, glycaemic control and biomarkers of complications

Paul J. Beisswenger

Biochem Soc Trans (2014) 42 (2): 450–456.

https://doi.org/10.1042/BST20130275

Published: 20 March 2014

... comprehensively determine the predictive value of these precise biomarkers, in the two of the most important diabetes outcome studies ever conducted. advanced glycation end-product (AGE) diabetic complication glycaemic fluctuation mass spectrometry metformin methylglyoxal The present review...

View article titled, Methylglyoxal in diabetes: link to treatment, glycaemic control and biomarkers of complications

Articles

Assay of methylglyoxal-derived protein and nucleotide AGEs

Naila Rabbani, Fozia Shaheen, Attia Anwar, Jinit Masania, Paul J. Thornalley

Biochem Soc Trans (2014) 42 (2): 511–517.

https://doi.org/10.1042/BST20140019

Published: 20 March 2014

... Journal compilation © 2014 Biochemical Society 2014 dicarbonyl stress glycation mass spectrometry methylglyoxal 3-nitrotyrosine oxidative stress 8-oxodeoxyguanosine Stable isotopic dilution analysis LC–MS/MS is also the method of choice to measure DNA glycation and oxidation adducts...

View article titled, Assay of methylglyoxal-derived protein and nucleotide AGEs

Articles

HDX-MS takes centre stage at unravelling kinase dynamics

Kristina Lorenzen, Tony Pawson

Biochem Soc Trans (2014) 42 (1): 145–150.

https://doi.org/10.1042/BST20130250

Published: 23 January 2014

... spectrometry (HDX-MS) mass spectrometry protein dynamics protein kinase HDX-MS has also suggested a resistance mechanism for its inhibitor Rp-cAMPS (Rp isomer of adenosine 3′,5′-cyclic monophosphorothioate) on the basis of an experiment comparing apo-PKA, PKA bound to a cAMP analogue and PKA bound...

View article titled, HDX-MS takes centre stage at unravelling kinase dynamics

Articles

Attempting to rewrite His tory: challenges with the analysis of histidine-phosphorylated peptides

Maria-Belen Gonzalez-Sanchez, Francesco Lanucara, Matthew Helm, Claire E. Eyers

Biochem Soc Trans (2013) 41 (4): 1089–1095.

https://doi.org/10.1042/BST20130072

Published: 18 July 2013

... equally to this paper. 2 To whom correspondence should be addressed (email Claire.Eyers@Liverpool.ac.uk ). 1 5 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 histidine mass spectrometry phosphate transfer phosphohistidine phosphorylation...

View article titled, Attempting to rewrite His tory: challenges with the analysis of histidine-phosphorylated peptides

Articles

Glycosylation of mouse and human immune cells: insights emerging from N-glycomics analyses

Aristotelis Antonopoulos, Simon J. North, Stuart M. Haslam, Anne Dell

Biochem Soc Trans (2011) 39 (5): 1334–1340.

https://doi.org/10.1042/BST0391334

Published: 21 September 2011

... Society 2011 congenital disorder of glycosylation congenital neutropenia glycogen storage disease 1b (GSD 1b) mass spectrometry matrix-assisted laser-desorption ionization–time-of-flight (MALDI–TOF) N-glycan Glycans attached to proteins and lipids on the surfaces of immune cells serve...

View article titled, Glycosylation of mouse and human immune cells: insights emerging from N-glycomics analyses

Articles

Analysis of oxidized and chlorinated lipids by mass spectrometry and relevance to signalling

Corinne M. Spickett, Norsyahida Mohd Fauzi

Biochem Soc Trans (2011) 39 (5): 1233–1239.

https://doi.org/10.1042/BST0391233

Published: 21 September 2011

... c.m.spickett@aston.ac.uk ). 24 5 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 chlorinated phospholipid inflammation mass spectrometry oxidized phospholipid (oxPL) precursor ion scanning Toll-like receptor (TLR) The interest in lipids as mediators...

View article titled, Analysis of oxidized and chlorinated lipids by mass spectrometry and relevance to signalling

Articles

Analysis of radicals and radical reaction products in cell signalling and biomolecular damage: the long hard road to gold-standard measures

Paul G. Winyard, Corinne M. Spickett, Helen R. Griffiths

Biochem Soc Trans (2011) 39 (5): 1217–1220.

https://doi.org/10.1042/BST0391217

Published: 21 September 2011

... area. 1 To whom correspondence should be addressed (email paul.winyard@pms.ac.uk ). 19 7 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 biomolecular damage cell signalling fluorescence free radical mass spectrometry measurement The present...

View article titled, Analysis of radicals and radical reaction products in cell signalling and biomolecular damage: the long hard road to gold-standard measures

Articles

Application of proteomics in the mechanistic study of traditional Chinese medicine

Xuan Liu, De-An Guo

Biochem Soc Trans (2011) 39 (5): 1348–1352.

https://doi.org/10.1042/BST0391348

Published: 21 September 2011

...@mail.shchc.ac.cn ). 29 6 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 mass spectrometry proteomics systems biology traditional Chinese medicine two-dimensional protein electrophoresis With a history of more than 2000 years, TCM (traditional Chinese medicine...

View article titled, Application of proteomics in the mechanistic study of traditional Chinese medicine

Articles

Contemporary techniques for detecting and identifying proteins susceptible to reversible thiol oxidation

Joseph R. Burgoyne, Philip Eaton

Biochem Soc Trans (2011) 39 (5): 1260–1267.

https://doi.org/10.1042/BST0391260

Published: 21 September 2011

... should be addressed (email philip.eaton@kcl.ac.uk ). 21 4 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 alkylating agent dibromobimane (DBB) glutaredoxin (Grx) mass spectrometry thiol oxidation thioredoxin (Trx) Cellular proteins can undergo...

View article titled, Contemporary techniques for detecting and identifying proteins susceptible to reversible thiol oxidation

Articles

Lipidomics of polyunsaturated-fatty-acid-derived oxygenated metabolites

Karen A. Massey, Anna Nicolaou

Biochem Soc Trans (2011) 39 (5): 1240–1246.

https://doi.org/10.1042/BST0391240

Published: 21 September 2011

... lipoxygenase (LOX) mass spectrometry polyunsaturated fatty acid (PUFA) PUFAs (polyunsaturated fatty acids) are important bioactive nutrients that exert a plethora of biological effects through their ability to alter the composition of cellular membranes, activate gene transcription and signalling...

View article titled, Lipidomics of polyunsaturated-fatty-acid-derived oxygenated metabolites

Articles

Glycoproteomics: a powerful tool for characterizing the diverse glycoforms of bacterial pilins and flagellins

Paul G. Hitchen, Katie Twigger, Esmeralda Valiente, Rebecca H. Langdon, Brendan W. Wren, Anne Dell

Biochem Soc Trans (2010) 38 (5): 1307–1313.

https://doi.org/10.1042/BST0381307

Published: 24 September 2010

... of the characteristic signature oxonium ion ( m / z 229) for DATDH. bacterium flagellin glycoproteomics glycosylation mass spectrometry pilin © The Authors Journal compilation © 2010 Biochemical Society 2010 14 12 2009 1 To whom correspondence should be addressed (email a.dell...

View article titled, Glycoproteomics: a powerful tool for characterizing the diverse glycoforms of bacterial pilins and flagellins

Articles

Interaction proteomics: characterization of protein complexes using tandem affinity purification–mass spectrometry

Pamela Völkel, Perrine Le Faou, Pierre-Olivier Angrand

Biochem Soc Trans (2010) 38 (4): 883–887.

https://doi.org/10.1042/BST0380883

Published: 26 July 2010

... tumour necrosis factor α 1 To whom correspondence should be addressed (email pierre-olivier.angrand@iri.univ-lille1.fr ). interaction proteomics mass spectrometry protein complex tandem affinity purification More than the proteins themselves, multimeric protein complexes...

View article titled, Interaction proteomics: characterization of protein complexes using tandem affinity purification–mass spectrometry

Articles

Development of a novel mass spectrometric technique for studying DNA damage

Tony L. Merrigan, C. Adam Hunniford, David J. Timson, Martin Catney, Robert W. McCullough

Biochem Soc Trans (2009) 37 (4): 905–909.

https://doi.org/10.1042/BST0370905

Published: 22 July 2009

... © The Authors Journal compilation © 2009 Biochemical Society 2009 desorption/ionization on silicon (DIOS) laser desorption mass spectrometry matrix-assisted laser-desorption ionization (MALDI) surface-assisted laser-desorption ionization (SALDI) Biological systems, particularly...

View article titled, Development of a novel mass spectrometric technique for studying DNA damage

Articles

Dynamic regulation of the voltage-gated Kv2.1 potassium channel by multisite phosphorylation

D.P. Mohapatra, K.-S. Park, J.S. Trimmer

Biochem Soc Trans (2007) 35 (5): 1064–1068.

https://doi.org/10.1042/BST0351064

Published: 25 October 2007

... The Authors Journal compilation © 2007 Biochemical Society 2007 calcineurin electrical signalling ion channel mass spectrometry neuron protein kinase Protein phosphorylation constitutes one of the major molecular mechanisms underlying plasticity of mammalian neurons [ 1 ]. Phosphorylation...

View article titled, Dynamic regulation of the voltage-gated Kv2.1 potassium channel by multisite phosphorylation

Articles

Structural and functional studies of defensin-inspired peptides

D.J. Clarke, D.J. Campopiano

Biochem Soc Trans (2006) 34 (2): 251–256.

https://doi.org/10.1042/BST0340251

Published: 20 March 2006

... correspondence should be addressed (email Dominic.Campopiano@ed.ac.uk ). 13 1 2006 © 2006 The Biochemical Society 2006 antimicrobial peptide defensin mass spectrometry The mammalian innate immune system produces a large array of weapons to protect the host from the constant attack...

View article titled, Structural and functional studies of defensin-inspired peptides

Articles

Interpreting correlations in metabolomic networks

R. Steuer, J. Kurths, O. Fiehn, W. Weckwerth

Biochem Soc Trans (2003) 31 (6): 1476–1478.

https://doi.org/10.1042/bst0311476

Published: 01 December 2003

... 2003 22 July 2003 © 2003 Biochemical Society 2003 data mining mass spectrometry metabolic networks metabolomics 1476 Biochemical Society Transactions (2003) Volume 31, part 6 Interpreting correlations in metabolomic networks R. Steuer*1, J. Kurths*, O. Fiehn and W. Weckwerth...

View article titled, Interpreting correlations in metabolomic networks

Articles

PLUNC (palate, lung and nasal epithelial clone) proteins in human nasal lavage fluid

B. Ghafouri, E. Kihlström, B. Ståhlbom, C. Tagesson, M. Lindahl

Biochem Soc Trans (2003) 31 (4): 810–814.

https://doi.org/10.1042/bst0310810

Published: 01 August 2003

..., the nasal and oral mucosa are constantly challenged by different environmental factors, such as micro- organisms, allergens, irritating particles and chemicals, that Key words: epoxy chemical, lipopolysaccharide, mass spectrometry, nasal lavage fluid, PLUNC (palate, lung and nasal epithelial clone), two...

View article titled, PLUNC (palate, lung and nasal epithelial clone) proteins in human nasal lavage fluid

Articles

The ProteinChip ® Biomarker System from Ciphergen Biosystems: a novel proteomics platform for rapid biomarker discovery and validation

K. Chapman

Biochem Soc Trans (2002) 30 (2): 82–87.

https://doi.org/10.1042/bst0300082

Published: 01 April 2002

...@ciphergen.com © 2002 Biochemical Society 2002 2-DE, two-dimensional protein gel electrophoresis Qq, quadropole-quadropole SELDI, surface-enhanced laser desorption/ionization TCC, transitional cell carcinoma TOF-MS, time-of-flight MS biomarker mass spectrometry protein biochip proteomics...

View article titled, The ProteinChip ® Biomarker System from Ciphergen Biosystems: a novel proteomics platform for rapid biomarker discovery and validation

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