Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library

Fert-Bober, Justyna; Venkatraman, Vidya; Hunter, Christie L.; Liu, Ruining; Crowgey, Erin L.; Pandey, Rakhi; Holewinski, Ronald J.; Stotland, Aleksandr; Berman, Benjamin P.; Eyk, Jennifer E. Van

doi:10.1021/acs.jproteome.9b00118

Cited by 34 publications

(67 citation statements)

References 53 publications

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“…48 Consistent with the report by Lee et al, 42 the largest number of citrullinated proteins in this study was found in the brain and lung. 48 In addition, unique cellular diversity of the citrullinated proteins suggests a broad biological role for protein citrullination. In summary, to pinpoint true-positive citrullination annotations, the citrullinated residue must be distinguished from deaminated residue.…”

Section: Hydrophobicity and Peptide Elusion In The Analysis Of Citrsupporting

confidence: 93%

“…To overcome this problem, Fert‐Bober et al came up with the idea of hypercitrullination library creation. The hypercitrullinated library allows for enrichment of the lower abundance citrullinated peptides to be detected by the DIA MS approach.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination In supporting

confidence: 81%

“…This series of analytical steps was shown to improve the specificity for identifying citrullinated residues and has been incorporated under one algorithm, Cit Finder, that is a robust tool for the correct assignment of protein citrullination in large data sets . Consistent with the report by Lee et al, the largest number of citrullinated proteins in this study was found in the brain and lung . In addition, unique cellular diversity of the citrullinated proteins suggests a broad biological role for protein citrullination.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination In mentioning

confidence: 97%

“…Decision tree summarizing the Cit Finder algorithm aiding the identification and validation of citrullinated peptides. To exploit and increase the correct assignment of protein citrullination rates, a decision tree algorithm to automate the identification of protein citrullination in large data sets was developed . The steps include using Lys‐C instead of trypsin for digestion, specifying deamidation as a variable modification, matching an unmodified‐modified pair to specify the RT shift, and specifying the neutral loss of 43 Da in the search engine.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination In mentioning

confidence: 97%

“…To exploit and increase the correct assignment of protein citrullination rates, a decision tree algorithm to automate the identification of protein citrullination in large data sets was developed. 48 The steps include using Lys-C instead of trypsin for digestion, specifying deamidation as a variable modification, matching an unmodifiedmodified pair to specify the RT shift, and specifying the neutral loss of 43 Da in the search engine. These steps are automated under the Cit Finder algorithm and are required for the correct assignment of protein citrullination in large data sets the peptide-spectrum matching is correct.…”

Section: Hydrophobicity and Peptide Elusion In The Analysis Of Citrmentioning

confidence: 99%

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Insights into the study and origin of the citrullinome in rheumatoid arthritis

Fert-Bober

Darrah

Andrade

2019

Immunological Reviews

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The presence of autoantibodies and autoreactive T cells to citrullinated proteins and citrullinating enzymes in patients with rheumatoid arthritis (RA), together with the accumulation of citrullinated proteins in rheumatoid joints, provides substantial evidence that dysregulated citrullination is a hallmark feature of RA. However, understanding mechanisms that dysregulate citrullination in RA has important challenges. Citrullination is a normal process in immune and non‐immune cells, which is likely activated by different conditions (eg, inflammation) with no pathogenic consequences. In a complex inflammatory environment such as the RA joint, unique strategies are therefore required to dissect specific mechanisms involved in the abnormal production of citrullinated proteins. Here, we will review current models of citrullination in RA and discuss critical components that, in our view, are relevant to understanding the accumulation of citrullinated proteins in the RA joint, collectively referred to as the RA citrullinome. In particular, we will focus on potential caveats in the study of citrullination in RA and will highlight methods to precisely detect citrullinated proteins in complex biological samples, which is a confirmatory approach to mechanistically link the RA citrullinome with unique pathogenic pathways in RA.

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Section: Hydrophobicity and Peptide Elusion In The Analysis Of Citrsupporting

confidence: 93%

Section: Mass Spectrometry Applied To the Study Of Citrullination In supporting

confidence: 81%

Section: Mass Spectrometry Applied To the Study Of Citrullination In mentioning

confidence: 97%

Section: Mass Spectrometry Applied To the Study Of Citrullination In mentioning

confidence: 97%

Section: Hydrophobicity and Peptide Elusion In The Analysis Of Citrmentioning

confidence: 99%

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Insights into the study and origin of the citrullinome in rheumatoid arthritis

Fert-Bober

Darrah

Andrade

2019

Immunological Reviews

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Data‐independent acquisition proteomics methods for analyzing post‐translational modifications

Yang

Qiao

2022

Proteomics

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Protein post‐translational modifications (PTMs) increase the functional diversity of the cellular proteome. Accurate and high throughput identification and quantification of protein PTMs is a key task in proteomics research. Recent advancements in data‐independent acquisition (DIA) mass spectrometry (MS) technology have achieved deep coverage and accurate quantification of proteins and PTMs. This review provides an overview of DIA data processing methods that cover three aspects of PTMs analysis, that is, detection of PTMs, site localization, and characterization of complex modification moieties, such as glycosylation. In addition, a survey of deep learning methods that boost DIA‐based PTMs analysis is presented, including in silico spectral library generation, as well as feature scoring and error rate control. The limitations and future directions of DIA methods for PTMs analysis are also discussed. Novel data analysis methods will take advantage of advanced MS instrumentation techniques to empower DIA MS for in‐depth and accurate PTMs measurements.

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Recent advances in characterization of citrullination and its implication in human disease research: From method development to network integration

Wang

Fields

2023

Proteomics

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Post‐translational modifications (PTM) of proteins increase the functional diversity of the proteome and have been implicated in the pathogenesis of numerous diseases. The most widely understood modifications include phosphorylation, methylation, acetylation, O‐linked/N‐linked glycosylation, and ubiquitination, all of which have been extensively studied and documented. Citrullination is a historically less explored, yet increasingly studied, protein PTM which has profound effects on protein conformation and protein‐protein interactions. Dysregulation of protein citrullination has been associated with disease development and progression. Identification and characterization of citrullinated proteins is highly challenging, complicated by the low cellular abundance of citrullinated proteins, making it difficult to identify and quantify the extent of citrullination in samples, coupled with challenges associated with development of mass spectrometry (MS)‐based methods, as the corresponding mass shift is relatively small, +0.984 Da, and identical to the mass shift of deamidation. The focus of this review is to discuss recent advancements of citrullination‐specific MS approaches and integration of the potential methodology for improved citrullination identification and characterization. In addition, the association of citrullination in disease networks is also highlighted.

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Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library

Cited by 34 publications

References 53 publications

Insights into the study and origin of the citrullinome in rheumatoid arthritis

Insights into the study and origin of the citrullinome in rheumatoid arthritis

Data‐independent acquisition proteomics methods for analyzing post‐translational modifications

Recent advances in characterization of citrullination and its implication in human disease research: From method development to network integration

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