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Fan SB, Meng JM, Lu S, Zhang K, Yang H, Chi H, Sun RX, Dong MQ, He SM. Using pLink to Analyze Cross-Linked Peptides. ACTA ACUST UNITED AC 2015; 49:8.21.1-8.21.19. [PMID: 25754995 DOI: 10.1002/0471250953.bi0821s49] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink.
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Affiliation(s)
- Sheng-Bo Fan
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jia-Ming Meng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shan Lu
- National Institute of Biological Sciences, Beijing, China
| | - Kun Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hao Yang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Rui-Xiang Sun
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
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Liu F, van Breukelen B, Heck AJR. Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Mol Cell Proteomics 2014; 13:2776-86. [PMID: 24980484 DOI: 10.1074/mcp.o114.039057] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disulfide bond identification is important for a detailed understanding of protein structures, which directly affect their biological functions. Here we describe an integrated workflow for the fast and accurate identification of authentic protein disulfide bridges. This novel workflow incorporates acidic proteolytic digestion using pepsin to eliminate undesirable disulfide reshuffling during sample preparation and a novel search engine, SlinkS, to directly identify disulfide-bridged peptides isolated via electron transfer higher energy dissociation (EThcD). In EThcD fragmentation of disulfide-bridged peptides, electron transfer dissociation preferentially leads to the cleavage of the S-S bonds, generating two intense disulfide-cleaved peptides as primary fragment ions. Subsequently, higher energy collision dissociation primarily targets unreacted and charge-reduced precursor ions, inducing peptide backbone fragmentation. SlinkS is able to provide the accurate monoisotopic precursor masses of the two disulfide-cleaved peptides and the sequence of each linked peptide by matching the remaining EThcD product ions against a linear peptide database. The workflow was validated using a protein mixture containing six proteins rich in natural disulfide bridges. Using this pepsin-based workflow, we were able to efficiently and confidently identify a total of 31 unique Cys-Cys bonds (out of 43 disulfide bridges present), with no disulfide reshuffling products detected. Pepsin digestion not only outperformed trypsin digestion in terms of the number of detected authentic Cys-Cys bonds, but, more important, prevented the formation of artificially reshuffled disulfide bridges due to protein digestion under neutral pH. Our new workflow therefore provides a precise and generic approach for disulfide bridge mapping, which can be used to study protein folding, structure, and stability.
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Affiliation(s)
- Fan Liu
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Bas van Breukelen
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Wu S, Brown JN, Tolić N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolić L. Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics 2014; 14:1211-22. [DOI: 10.1002/pmic.201300378] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/10/2014] [Accepted: 02/25/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Si Wu
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Joseph N. Brown
- Biological Sciences Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Da Meng
- Computational Mathematics Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Xiaowen Liu
- Department of BioHealth Informatics; Indiana University-Purdue University Indianapolis; Indianapolis IN USA
| | - Haizhen Zhang
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Ronald J. Moore
- Biological Sciences Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Pavel Pevzner
- Department of Computer Science and Engineering; University of California, San Diego; La Jolla CA USA
| | - Richard D. Smith
- Biological Sciences Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
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Abidi F, Chobert JM, Haertlé T, Marzouki MN. Purification and biochemical characterization of stable alkaline protease Prot-2 from Botrytis cinerea. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.09.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Shen Y, Tolić N, Xie F, Zhao R, Purvine SO, Schepmoes AA, Ronald JM, Anderson GA, Smith RD. Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods. J Proteome Res 2011; 10:3929-43. [PMID: 21678914 PMCID: PMC3166380 DOI: 10.1021/pr200052c] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report on the effectiveness of CID, HCD, and ETD for LC-FT MS/MS analysis of peptides using a tandem linear ion trap-Orbitrap mass spectrometer. A range of software tools and analysis parameters were employed to explore the use of CID, HCD, and ETD to identify peptides (isolated from human blood plasma) without the use of specific "enzyme rules". In the evaluation of an FDR-controlled SEQUEST scoring method, the use of accurate masses for fragments increased the number of identified peptides (by ~50%) compared to the use of conventional low accuracy fragment mass information, and CID provided the largest contribution to the identified peptide data sets compared to HCD and ETD. The FDR-controlled Mascot scoring method provided significantly fewer peptide identifications than SEQUEST (by 1.3-2.3 fold) and CID, HCD, and ETD provided similar contributions to identified peptides. Evaluation of de novo sequencing and the UStags method for more intense fragment ions revealed that HCD afforded more contiguous residues (e.g., ≥ 7 amino acids) than either CID or ETD. Both the FDR-controlled SEQUEST and Mascot scoring methods provided peptide data sets that were affected by the decoy database used and mass tolerances applied (e.g., identical peptides between data sets could be limited to ~70%), while the UStags method provided the most consistent peptide data sets (>90% overlap). The m/z ranges in which CID, HCD, and ETD contributed the largest number of peptide identifications were substantially overlapping. This work suggests that the three peptide ion fragmentation methods are complementary and that maximizing the number of peptide identifications benefits significantly from a careful match with the informatics tools and methods applied. These results also suggest that the decoy strategy may inaccurately estimate identification FDRs.
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Affiliation(s)
- Yufeng Shen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Fang Xie
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - J. Moore Ronald
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Gordon A. Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
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Shen Y, Tolić N, Liu T, Zhao R, Petritis BO, Gritsenko MA, Camp DG, Moore RJ, Purvine SO, Esteva FJ, Smith RD. Blood peptidome-degradome profile of breast cancer. PLoS One 2010; 5:e13133. [PMID: 20976186 PMCID: PMC2956627 DOI: 10.1371/journal.pone.0013133] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 09/06/2010] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Cancer invasion and metastasis are closely associated with activities within the degradome; however, little is known about whether these activities can be detected in the blood of cancer patients. METHODOLOGY AND PRINCIPAL FINDINGS The peptidome-degradome profiles of pooled blood plasma sampled from 15 breast cancer patients (BCP) and age, race, and menopausal status matched control healthy persons (HP) were globally characterized using advanced comprehensive separations combined with tandem Fourier transform mass spectrometry and new data analysis approaches that facilitated top-down peptidomic analysis. The BCP pool displayed 71 degradome protein substrates that encompassed 839 distinct peptidome peptides. In contrast, the HP 50 degradome substrates found encompassed 425 peptides. We find that the ratios of the peptidome peptide relative abundances can vary as much as >4000 fold between BCP and HP. The experimental results also show differential degradation of substrates in the BCP sample in their functional domains, including the proteolytic and inhibitory sites of the plasmin-antiplasmin and thrombin-antithrombin systems, the main chains of the extracellular matrix protection proteins, the excessive degradation of innate immune system key convertases and membrane attack complex components, as well as several other cancer suppressor proteins. CONCLUSIONS Degradomics-peptidomics profiling of blood plasma is highly sensitive to changes not evidenced by conventional bottom-up proteomics and potentially provides unique signatures of possible diagnostic utility.
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Affiliation(s)
- Yufeng Shen
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Tao Liu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Brianne O. Petritis
- Biological Design Interdisciplinary Graduate Degree Program, Arizona State University, Tempe, Arizona, United States of America
| | - Marina A. Gritsenko
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David G. Camp
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ronald J. Moore
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Francisco J. Esteva
- Departments of Breast Medical Oncology and Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Richard D. Smith
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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