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Article ; Online: TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data.

Walzer, Mathias / Jeong, Kyowon / Tabb, David L / Vizcaíno, Juan Antonio

2023 Volume 24, Issue 3-4, Page(s) e2200403

Abstract: Although Top-down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise their adoption. In this context, there are numerous ... ...

Abstract	Although Top-down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise their adoption. In this context, there are numerous improvements that are possible in the area of open science practices, including a greater application of the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. These include, for example, increased data sharing practices and readily available open data standards. Additionally, the field would benefit from the development of open data analysis workflows that can enable data reuse of public datasets, something that is increasingly common in other proteomics fields.
MeSH term(s)	Proteomics/methods ; Proteins/analysis ; Workflow
Chemical Substances	Proteins
Language	English
Publishing date	2023-10-03
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200403
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Article: Comparative Proteomics Analysis between Maize and Sorghum Uncovers Important Proteins and Metabolic Pathways Mediating Drought Tolerance.

Ali, Ali Elnaeim Elbasheir / Husselmann, Lizex Hollenbach / Tabb, David L / Ludidi, Ndiko

Life (Basel, Switzerland)

2023 Volume 13, Issue 1

Abstract: Drought severely affects crop yield and yield stability. Maize and sorghum are major crops in Africa and globally, and both are negatively impacted by drought. However, sorghum has a better ability to withstand drought than maize. Consequently, this ... ...

Abstract	Drought severely affects crop yield and yield stability. Maize and sorghum are major crops in Africa and globally, and both are negatively impacted by drought. However, sorghum has a better ability to withstand drought than maize. Consequently, this study identifies differences between maize and sorghum grown in water deficit conditions, and identifies proteins associated with drought tolerance in these plant species. Leaf relative water content and proline content were measured, and label-free proteomics analysis was carried out to identify differences in protein expression in the two species in response to water deficit. Water deficit enhanced the proline accumulation in sorghum roots to a higher degree than in maize, and this higher accumulation was associated with enhanced water retention in sorghum. Proteomic analyses identified proteins with differing expression patterns between the two species, revealing key metabolic pathways that explain the better drought tolerance of sorghum than maize. These proteins include phenylalanine/tyrosine ammonia-lyases, indole-3-acetaldehyde oxidase, sucrose synthase and phenol/catechol oxidase. This study highlights the importance of phenylpropanoids, sucrose, melanin-related metabolites and indole acetic acid (auxin) as determinants of the differences in drought stress tolerance between maize and sorghum. The selection of maize and sorghum genotypes with enhanced expression of the genes encoding these differentially expressed proteins, or genetically engineering maize and sorghum to increase the expression of such genes, can be used as strategies for the production of maize and sorghum varieties with improved drought tolerance.
Language	English
Publishing date	2023-01-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life13010170
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Article ; Online: The SEQUEST family tree.

Tabb, David L

Journal of the American Society for Mass Spectrometry

2015 Volume 26, Issue 11, Page(s) 1814–1819

Abstract: Since its introduction in 1994, SEQUEST has gained many important new capabilities, and a host of successor algorithms have built upon its successes. This Account and Perspective maps the evolution of this important tool and charts the relationships ... ...

Abstract	Since its introduction in 1994, SEQUEST has gained many important new capabilities, and a host of successor algorithms have built upon its successes. This Account and Perspective maps the evolution of this important tool and charts the relationships among contributions to the SEQUEST legacy. Many of the changes represented improvements in computing speed by clusters and graphics cards. Mass spectrometry innovations in mass accuracy and activation methods led to shifts in fragment modeling and scoring strategies. These changes, as well as the movement of laboratories and lab members, have led to great diversity among the members of the SEQUEST family. Graphical Abstract ᅟ.
MeSH term(s)	Algorithms ; Proteomics ; Software ; Tandem Mass Spectrometry
Language	English
Publishing date	2015-06-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1007/s13361-015-1201-3
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Article: A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant

Gabier, Hawwa / Tabb, David L / Farrant, Jill M / Rafudeen, Mohamed Suhail

Life (Basel, Switzerland)

2021 Volume 11, Issue 11

Abstract: Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its ... ...

Abstract	Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology approach. The aim of the current study was to conduct a label-free proteomic analysis of leaves of the resurrection plant
Language	English
Publishing date	2021-11-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life11111242
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Article ; Online: MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.

Potgieter, Matthys G / Nel, Andrew J M / Fortuin, Suereta / Garnett, Shaun / Wendoh, Jerome M / Tabb, David L / Mulder, Nicola J / Blackburn, Jonathan M

PLoS computational biology

2023 Volume 19, Issue 6, Page(s) e1011163

Abstract: Background: Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations ... ...

Abstract	Background: Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines. Results: We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database-but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation. Conclusions: By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.
MeSH term(s)	Humans ; Tandem Mass Spectrometry ; RNA, Ribosomal, 16S/genetics ; Databases, Protein ; Peptides/genetics ; Peptides/analysis ; Microbiota/genetics ; Bacteria/genetics ; Proteome/genetics
Chemical Substances	RNA, Ribosomal, 16S ; Peptides ; Proteome
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011163
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Article ; Online: Evaluating protein interactions through cross-linking mass spectrometry.

Tabb, David L

Nature methods

2012 Volume 9, Issue 9, Page(s) 879–881

MeSH term(s)	Animals ; Cross-Linking Reagents/chemistry ; Humans ; Mass Spectrometry/methods ; Peptides/analysis ; Peptides/chemistry ; Proteomics/methods
Chemical Substances	Cross-Linking Reagents ; Peptides
Language	English
Publishing date	2012-08-30
Publishing country	United States
Document type	News ; Comment
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/nmeth.2139
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Article ; Online: Quality assessment for clinical proteomics.

Tabb, David L

Clinical biochemistry

2012 Volume 46, Issue 6, Page(s) 411–420

Abstract: Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling ...

Abstract	Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling batch effects properly. New efforts have produced sets of performance metrics and measurements of variability that establish sound expectations for experiments in clinical proteomics. As researchers begin incorporating these metrics in a quality by design paradigm, the variability of individual steps in experimental pipelines will be reduced, regularizing overall outcomes. This review discusses the evolution of quality assessment in 2D gel electrophoresis, mass spectrometry-based proteomic profiling, tandem mass spectrometry-based protein inventories, and proteomic quantitation. Taken together, the advances in each of these technologies are establishing databases that will be increasingly useful for decision-making in clinical experimentation.
MeSH term(s)	Chromatography, Liquid ; Clinical Laboratory Techniques/methods ; Computational Biology ; Gene Expression Profiling ; Humans ; Medical Laboratory Science ; Proteomics/methods ; Quality Control ; Tandem Mass Spectrometry/methods
Language	English
Publishing date	2012-12-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	390372-2
ISSN	1873-2933 ; 0009-9120
ISSN (online)	1873-2933
ISSN	0009-9120
DOI	10.1016/j.clinbiochem.2012.12.003
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Article: Proteomic Identification and Meta-Analysis in

Klein, Ashwil / Husselmann, Lizex H H / Williams, Achmat / Bell, Liam / Cooper, Bret / Ragar, Brent / Tabb, David L

Plants (Basel, Switzerland)

2021 Volume 10, Issue 4

Abstract: While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought ... ...

Abstract	While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity "genes" varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order
Language	English
Publishing date	2021-04-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10040765
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Article ; Online: Dysregulated healing responses in diabetic wounds occur in the early stages postinjury.

Boodhoo, Kiara / Vlok, Mare / Tabb, David L / Myburgh, Kathryn H / van de Vyver, Mari

Journal of molecular endocrinology

2020 Volume 66, Issue 2, Page(s) 141–155

Abstract: Chronic wounds are a serious and debilitating complication of diabetes. A better understanding of the dysregulated healing responses following injury will provide insight into the optimal time frame for therapeutic intervention. In this study, a direct ... ...

Abstract	Chronic wounds are a serious and debilitating complication of diabetes. A better understanding of the dysregulated healing responses following injury will provide insight into the optimal time frame for therapeutic intervention. In this study, a direct comparison was done between the healing dynamics and the proteome of acute and obese diabetic wounds on days 2 and 7 following injury. Full thickness excisional wounds were induced on obese diabetic (B6.Cg-lepob/J, ob/ob, n = 14) (blood glucose 423.25 ± 127.92 mg/dL) and WT control (C57BL/6J, n = 14) (blood glucose 186.67 ± 24.5 mg/dL) mice. Histological analysis showed no signs of healing in obese DM wounds whereas complete wound closure/re-epithelisation, the formation of granulation tissue and signs of re-vascularisation, was evident in acute wounds on day 7. In obese DM wounds, substance P deficiency and increased MMP-9 activity on day 2 coincided with increased cytokine/chemokine levels within wound fluid. LC-MS/MS identified 906 proteins, of which 23 (Actn3, Itga6, Epb41, Sncg, Nefm, Rsp18, Rsp19, Rpl22, Macroh2a1, Rpn1, Ppib, Snrnp70, Ddx5, Eif3g, Tpt1, FABP5, Cavin1, Stfa1, Stfa3, Cycs, Tkt, Mb, Chmp2a) were differentially expressed in wounded tissue on day 2 (P < 0.05; more than two-fold) and 6 (Cfd, Ptms, Hp, Hmga1, Cbx3, Syap1) (P < 0.05; more than two-fold) on day 7. A large number of dysregulated proteins on day 2 was associated with an inability to progress into the proliferative stage of healing and suggest that early intervention might be pivotal for effective healing outcomes. The proteomic approach highlighted the complexity of obese DM wounds in which the dysregulation involves multiple regulatory pathways and biological processes.
MeSH term(s)	Animals ; Body Fluids/metabolism ; Chronic Disease ; Cytokines/metabolism ; Diabetes Mellitus, Experimental/pathology ; Matrix Metalloproteinase 9/metabolism ; Mice, Inbred C57BL ; Mice, Obese ; Proteome/metabolism ; Substance P/metabolism ; Wound Healing ; Wounds and Injuries/pathology ; Mice
Chemical Substances	Cytokines ; Proteome ; Substance P (33507-63-0) ; Matrix Metalloproteinase 9 (EC 3.4.24.35)
Language	English
Publishing date	2020-12-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	645012-x
ISSN	1479-6813 ; 0952-5041
ISSN (online)	1479-6813
ISSN	0952-5041
DOI	10.1530/JME-20-0256
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Article ; Online: A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant Xerophyta schlechteri during Dehydration

Hawwa Gabier / David L. Tabb / Jill M. Farrant / Mohamed Suhail Rafudeen

Life, Vol 11, Iss 1242, p

2021 Volume 1242

Abstract	Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology approach. The aim of the current study was to conduct a label-free proteomic analysis of leaves of the resurrection plant Xerophyta schlechteri in response to desiccation. A targeted metabolomics approach was validated and correlated to the proteomics, contributing the missing link in studies on this species. Three physiological stages were identified: an early response to drying, during which the leaf tissues declined from full turgor to a RWC of ~80–70%, a mid-response in which the RWC declined to 40% and a late response where the tissues declined to 10% RWC. We identified 517 distinct proteins that were differentially expressed, of which 253 proteins were upregulated and 264 were downregulated in response to the three drying stages. Metabolomics analyses, which included monitoring the levels of a selection of phytohormones, amino acids, sugars, sugar alcohols, fatty acids and organic acids in response to dehydration, correlated with some of the proteomic differences, giving insight into the biological processes apparently involved in desiccation tolerance in this species.
Keywords	dehydration ; desiccation tolerance ; plant proteomics ; label-free quantification ; metabolomics ; resurrection plant ; Science ; Q
Subject code	580
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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