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Literature DB >> 30295672

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine.

Hao Chi^1,2, Chao Liu^1,2, Hao Yang^1,2, Wen-Feng Zeng^1,2, Long Wu^1,2, Wen-Jing Zhou^1,2, Rui-Min Wang^1,2, Xiu-Nan Niu^1,2, Yue-He Ding³, Yao Zhang^4,5, Zhao-Wei Wang^1,2, Zhen-Lin Chen^1,2, Rui-Xiang Sun^1,2, Tao Liu¹, Guang-Ming Tan¹, Meng-Qiu Dong³, Ping Xu⁴, Pei-Heng Zhang¹, Si-Min He^1,2.

Abstract

We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70-85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.

Entities: Species

Year: 2018 PMID： 30295672 DOI： 10.1038/nbt.4236

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

32 in total

1. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model.

Authors: David L Tabb; Anita Saraf; John R Yates
Journal: Anal Chem Date: 2003-12-01 Impact factor: 6.986

2. A method for reducing the time required to match protein sequences with tandem mass spectra.

Authors: Robertson Craig; Ronald C Beavis
Journal: Rapid Commun Mass Spectrom Date: 2003 Impact factor: 2.419

3. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?

Authors: Robert J Chalkley; Peter R Baker; Kirk C Hansen; Katalin F Medzihradszky; Nadia P Allen; Michael Rexach; Alma L Burlingame
Journal: Mol Cell Proteomics Date: 2005-05-27 Impact factor: 5.911

4. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

Authors: Annette Michalski; Juergen Cox; Matthias Mann
Journal: J Proteome Res Date: 2011-02-28 Impact factor: 4.466

5. Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.

Authors: Yue-He Ding; Zhou Gong; Xu Dong; Kan Liu; Zhu Liu; Chao Liu; Si-Min He; Meng-Qiu Dong; Chun Tang
Journal: J Biol Chem Date: 2016-12-19 Impact factor: 5.157

6. Error-tolerant identification of peptides in sequence databases by peptide sequence tags.

Authors: M Mann; M Wilm
Journal: Anal Chem Date: 1994-12-15 Impact factor: 6.986

7. Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation.

Authors: Inamul Hasan Madar; Seung-Ik Ko; Hokeun Kim; Dong-Gi Mun; Sangtae Kim; Richard D Smith; Sang-Won Lee
Journal: Anal Chem Date: 2016-12-22 Impact factor: 6.986

8. Cell type- and brain region-resolved mouse brain proteome.

Authors: Kirti Sharma; Sebastian Schmitt; Caroline G Bergner; Stefka Tyanova; Nirmal Kannaiyan; Natalia Manrique-Hoyos; Karina Kongi; Ludovico Cantuti; Uwe-Karsten Hanisch; Mari-Anne Philips; Moritz J Rossner; Matthias Mann; Mikael Simons
Journal: Nat Neurosci Date: 2015-11-02 Impact factor: 24.884

9. A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.

Authors: Joel M Chick; Deepak Kolippakkam; David P Nusinow; Bo Zhai; Ramin Rad; Edward L Huttlin; Steven P Gygi
Journal: Nat Biotechnol Date: 2015-06-15 Impact factor: 54.908

10. The potential clinical impact of the release of two drafts of the human proteome.

Authors: Iakes Ezkurdia; Enrique Calvo; Angela Del Pozo; Jesús Vázquez; Alfonso Valencia; Michael L Tress
Journal: Expert Rev Proteomics Date: 2015-10-23 Impact factor: 3.940

54 in total

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

Authors: Hao Yang; Yan-Chang Li; Ming-Zhi Zhao; Fei-Lin Wu; Xi Wang; Wei-Di Xiao; Yi-Hao Wang; Jun-Ling Zhang; Fu-Qiang Wang; Feng Xu; Wen-Feng Zeng; Christopher M Overall; Si-Min He; Hao Chi; Ping Xu
Journal: Mol Cell Proteomics Date: 2019-01-08 Impact factor: 5.911

2. Persulfidation-based Modification of Cysteine Desulfhydrase and the NADPH Oxidase RBOHD Controls Guard Cell Abscisic Acid Signaling.

Authors: Jie Shen; Jing Zhang; Mingjian Zhou; Heng Zhou; Beimi Cui; Cecilia Gotor; Luis C Romero; Ling Fu; Jing Yang; Christine Helen Foyer; Qiaona Pan; Wenbiao Shen; Yanjie Xie
Journal: Plant Cell Date: 2020-02-05 Impact factor: 11.277

3. HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells.

Authors: Shan Lu; Kelsey Gasior; Haiyang Yu; Digvijay Singh; Sonia Vazquez-Sanchez; Olga Tapia; Divek Toprani; Melinda S Beccari; John R Yates; Sandrine Da Cruz; Jay M Newby; Miguel Lafarga; Amy S Gladfelter; Elizabeth Villa; Don W Cleveland
Journal: Science Date: 2020-12-17 Impact factor: 47.728

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine.

1. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model.

2. A method for reducing the time required to match protein sequences with tandem mass spectra.

3. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?

4. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

5. Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.

6. Error-tolerant identification of peptides in sequence databases by peptide sequence tags.

7. Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation.

8. Cell type- and brain region-resolved mouse brain proteome.

9. A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.

10. The potential clinical impact of the release of two drafts of the human proteome.

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

2. Persulfidation-based Modification of Cysteine Desulfhydrase and the NADPH Oxidase RBOHD Controls Guard Cell Abscisic Acid Signaling.

3. HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells.

4. Efficient mitotic checkpoint signaling depends on integrated activities of Bub1 and the RZZ complex.

5. A Chemical Strategy for Protease Substrate Profiling.

6. Crystal-C: A Computational Tool for Refinement of Open Search Results.

7. SlFERL Interacts with S-Adenosylmethionine Synthetase to Regulate Fruit Ripening.

8. DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results.

9. Spatiotemporally resolved subcellular phosphoproteomics.

10. Pre-termination Transcription Complex: Structure and Function.