Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics

Yang, Hao; Li, Yanchang; Zhao, Mingzhi; Wu, Feilin; Wang, Xi; Xiao, Weidi; Wang, Yihao; Zhang, Junling; Wang, Fuqiang; Xu, Feng; Zeng, Wenfeng; Overall, Christopher M.; He, Shan; Chi, Hao; Xu, Ping

doi:10.1074/mcp.tir118.000918

Cited by 37 publications

(37 citation statements)

References 48 publications

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“…Gaps in the b and y ion series of the trypsin spectra can be filled in using the Ac‐LysargiNase spectra and vice versa which results in fuller coverage of the peptide. The authors of this method 42 found that in a test set of Escherichia coli proteome samples around 50% of the peptides had both trypsin and Ac‐LysargiNase spectra, and the mirror spectra were able to reach 97% coverage of either the y or b ion series 42 . They created the software tool pNovoM to pair mirror spectra and perform the de novo search.…”

Section: Data Acquisition and Sample Preparation Methods For Improvinmentioning

confidence: 99%

“…40 Yang et al have shown how using complementary enzymes can produce what they call mirror spectra. 42 Mirror spectra can be produced by digesting the sample (in parallel reactions) with trypsin (which cuts the peptide bond C-terminal to lysine and arginine residues) and LysargiNase (which cuts on the N-terminal side of lysine and arginine residues). This results in paired sets of peptides that differ only by having a basic residue at the Nor the C-terminus, called mirror peptides.…”

Section: Distinguishing Fragment Ion Typesmentioning

confidence: 99%

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Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification

2020

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Mass spectrometry‐based proteomics is a popular and powerful method for precise and highly multiplexed protein identification. The most common method of analyzing untargeted proteomics data is called database searching, where the database is simply a collection of protein sequences from the target organism, derived from genome sequencing. Experimental peptide tandem mass spectra are compared to simplified models of theoretical spectra calculated from the translated genomic sequences. However, in several interesting application areas, such as forensics, archaeology, venomics, and others, a genome sequence may not be available, or the correct genome sequence to use is not known. In these cases, de novo peptide identification can play an important role. De novo methods infer peptide sequence directly from the tandem mass spectrum without reference to a sequence database, usually using graph‐based or machine learning algorithms. In this review, we provide a basic overview of de novo peptide identification methods and applications, briefly covering de novo algorithms and tools, and focusing in more depth on recent applications from venomics, metaproteomics, forensics, and characterization of antibody drugs.

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Section: Data Acquisition and Sample Preparation Methods For Improvinmentioning

confidence: 99%

Section: Distinguishing Fragment Ion Typesmentioning

confidence: 99%

Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification

2020

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“…Furthermore, precise de novo peptide sequencing is hindered by poor coverage of b and/or y ion series, which is a common problem in SUMOylation identification by MS. Recently, a protein digestive enzyme Ac‐LysargiNase has been reported to provide a better coverage and stronger signal of b ions compared to tryptic peptides , it also can work with trypsin to create a complementary ion series. So, the application of Ac‐LysargiNase in SUMOylation identification is also a technical improvement.…”

Section: Perspectivesmentioning

confidence: 99%

MS‐based strategies for identification of protein SUMOylation modification

Sheng

Wang

et al. 2019

Electrophoresis

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Protein SUMOylation modification conjugated with small ubiquitin-like modifiers (SUMOs) is one kind of PTMs, which exerts comprehensive roles in cellular functions, including gene expression regulation, DNA repair, intracellular transport, stress responses, and tumorigenesis. With the development of the peptide enrichment approaches and MS technology, more than 6000 SUMOylated proteins and about 40 000 SUMO acceptor sites have been identified. In this review, we summarize several popular approaches that have been developed for the identification of SUMOylated proteins in human cells, and further compare their technical advantages and disadvantages. And we also introduce identification approaches of target proteins which are co-modified by both SUMOylation and ubiquitylation. We highlight the emerging trends in the SUMOylation field as well. Especially, the advent of the clustered regularly interspaced short palindromic repeats/ Cas9 technique will facilitate the development of MS for SUMOylation identification.

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“…A large variety of informatics tools have been developed to aid in assay development and to process the data collected by various acquisition types [14,15]. Novel bioinformatics tools include quality control algorithms [16], de novo peptide sequencing [17], and webbased resources for dissemination of results [18].…”

Section: Introductionmentioning

confidence: 99%

Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications

Pino

Rose

O’Broin

et al. 2020

Biochemical Society Transactions

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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 proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein–protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.

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Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics

Cited by 37 publications

References 48 publications

Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification

Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification

MS‐based strategies for identification of protein SUMOylation modification

Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications

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