Database independent proteomics analysis of the ostrich and human proteome

Altelaar, Maarten; Navarro, D. G.; Boekhorst, Jos; Breukelen, Bas van; Snel, Berend; Mohammed, Shabaz; Heck, Albert J. R.

doi:10.1073/pnas.1108399108

Cited by 12 publications

(8 citation statements)

References 45 publications

(50 reference statements)

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“…S5). These findings are in line with previous reports describing that peptides with a strong basic N terminus generate more straightforward and easy-to-interpret MS/MS spectra in ETD (19).…”

Section: Resultssupporting

confidence: 92%

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

Mommen

Frese

Meiring

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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174

205

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The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification of HLA class I-associated peptides. However, the HLA class I peptide repertoire remains largely unexplored because the variable nature of endogenous peptides represents difficulties in conventional peptide fragmentation technology. Here, we substantially enhanced (about threefold) the identification success rate of peptides presented by HLA class I using combined electron-transfer/higher-energy collision dissociation (EThcD), reporting over 12,000 high-confident (false discovery rate <1%) peptides from a single human B-cell line. The direct importance of such an unprecedented large dataset is highlighted by the discovery of unique features in antigen presentation. The observation that a substantial part of proteins is sampled across different HLA alleles, and the common occurrence of HLA class I nested sets, suggest that the constraints of HLA class I to comprehensively present the health states of cells are not as tight as previously thought. Our dataset contains a substantial set of peptides bearing a variety of posttranslational modifications presented with marked allele-specific differences. We propose that EThcD should become the method of choice in analyzing HLA class I-presented peptides.human leukocyte antigen class I | electron-transfer dissociation | major histocompatibility complex | phosphorylation | binding motif C lass I molecules of the human leukocyte antigen (HLA) complex present short peptides, typically 8-11 aa in length at the cell surface, for scrutiny by the immune system (1). These peptide fragments are generated in the cytoplasm by proteasomal degradation of source proteins, translocated into the endoplasmic reticulum (ER) and subjected to N-terminal trimming to a size that is suitable for loading onto the HLA (2). Loading is governed by physicochemical binding motifs typical for each HLA class I allele (3). Depending on the motif required for the HLA class I allele(s) expressed, an ER-residing peptide may become presented or not. Recognition of specific HLA class I peptide complexes by CD8 T lymphocytes on pathogen infected or cancerous cells leads to the activation of a cytotoxic response and the clearance of the diseased cell. The identification of these HLA class I-associated peptides has important consequences for understanding the biology of cells, vaccine design, and tumor immunotherapy (4, 5).Today mass spectrometry (MS) is the core technology for the analysis of HLA class I-presented peptides. These peptides are typically enriched from cell lysates through the affinity purification of HLA class I peptide complexes, released from the HLA by acid elution, and separated by liquid chromatography (LC) before introduction into the mass spectrometer. Identification is commonly accomplished by...

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Section: Resultssupporting

confidence: 92%

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

Mommen

Frese

Meiring

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

174

205

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“…We previously showed that peptides that carry two protons at the N-terminus fragment predominantly into N-terminal c fragment ions during electron-transfer dissociation (ETD), facilitating straightforward peptide sequencing even when no a priori knowledge of the protein sequence is available. , Here, we analyzed thousands of peptides generated by LysargiNase or trypsin from a Jurkat cell lysate using ETD or HCD to investigate whether LysargiNase represents a suitable protease for ladder sequencing of peptides. We describe the fragmentation characteristics of these K/R(X) n (i.e., LysargiNase) and (X) n K/R (i.e., trypsin) peptides during chromatographic separation and gas-phase fragmentation and show the consequences of mirroring the location of the basic residue on peptide fragmentation, with the aim of probing the broader usability of LysargiNase in (phospho)proteomics applications.…”

Section: Introductionmentioning

confidence: 99%

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)_n and (X)_nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics

Tsiatsiani¹,

Giansanti²,

Scheltema³

et al. 2016

J. Proteome Res.

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A key step in shotgun proteomics is the digestion of proteins into peptides amenable for mass spectrometry. Tryptic peptides can be readily sequenced and identified by collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD) because the fragmentation rules are well-understood. Here, we investigate LysargiNase, a perfect trypsin mirror protease, because it cleaves equally specific at arginine and lysine residues, albeit at the N-terminal end. LysargiNase peptides are therefore practically tryptic-like in length and sequence except that following ESI, the two protons are now both positioned at the N-terminus. Here, we compare side-by-side the chromatographic separation properties, gas-phase fragmentation characteristics, and (phospho)proteome sequence coverage of tryptic (i.e., (X)K/R) and LysargiNase (i.e., K/R(X)) peptides using primarily electron-transfer dissociation (ETD) and, for comparison, HCD. We find that tryptic and LysargiNase peptides fragment nearly as mirror images. For LysargiNase predominantly N-terminal peptide ions (c-ions (ETD) and b-ions (HCD)) are formed, whereas for trypsin, C-terminal fragment ions dominate (z-ions (ETD) and y-ions (HCD)) in a homologous mixture of complementary ions. Especially during ETD, LysargiNase peptides fragment into low-complexity but information-rich sequence ladders. Trypsin and LysargiNase chart distinct parts of the proteome, and therefore, the combined use of these enzymes will benefit a more in-depth and reliable analysis of (phospho)proteomes.

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“…Proteins can also interact with other molecules like RNA, DNA and metabolites. These complexes play crucial roles in regulatory processes, signalling cascades, cellular functions, and their inability to interact can result in their function being lost ( Altelaar et al, 2012 ; Ma and Johnson, 2012 ). Tranche is one of the few public repositories that can manage this type of data at the moment, and it is based on an encrypted peer-to-peer system that stores data in numerous servers across the world.…”

Section: Proteomicsmentioning

confidence: 99%

Innovative in Silico Approaches for Characterization of Genes and Proteins

et al. 2022

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Bioinformatics is an amalgamation of biology, mathematics and computer science. It is a science which gathers the information from biology in terms of molecules and applies the informatic techniques to the gathered information for understanding and organizing the data in a useful manner. With the help of bioinformatics, the experimental data generated is stored in several databases available online like nucleotide database, protein databases, GENBANK and others. The data stored in these databases is used as reference for experimental evaluation and validation. Till now several online tools have been developed to analyze the genomic, transcriptomic, proteomics, epigenomics and metabolomics data. Some of them include Human Splicing Finder (HSF), Exonic Splicing Enhancer Mutation taster, and others. A number of SNPs are observed in the non-coding, intronic regions and play a role in the regulation of genes, which may or may not directly impose an effect on the protein expression. Many mutations are thought to influence the splicing mechanism by affecting the existing splice sites or creating a new sites. To predict the effect of mutation (SNP) on splicing mechanism/signal, HSF was developed. Thus, the tool is helpful in predicting the effect of mutations on splicing signals and can provide data even for better understanding of the intronic mutations that can be further validated experimentally. Additionally, rapid advancement in proteomics have steered researchers to organize the study of protein structure, function, relationships, and dynamics in space and time. Thus the effective integration of all of these technological interventions will eventually lead to steering up of next-generation systems biology, which will provide valuable biological insights in the field of research, diagnostic, therapeutic and development of personalized medicine.

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Database independent proteomics analysis of the ostrich and human proteome

Cited by 12 publications

References 45 publications

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)_n and (X)_nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics

Innovative in Silico Approaches for Characterization of Genes and Proteins

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Database independent proteomics analysis of the ostrich and human proteome

Cited by 12 publications

References 45 publications

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)n and (X)nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics

Innovative in Silico Approaches for Characterization of Genes and Proteins

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Product

Resources

About

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)_n and (X)_nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics