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Literature DB >> 26154010

Illuminating the dark matter of shotgun proteomics.

Owen S Skinner¹, Neil L Kelleher².

Abstract

Mesh：

Substances：
Peptides

Year: 2015 PMID： 26154010 DOI： 10.1038/nbt.3287

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

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4 in total

1. Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics.

Authors: Michael L Nielsen; Mikhail M Savitski; Roman A Zubarev
Journal: Mol Cell Proteomics Date: 2006-10-02 Impact factor: 5.911

2. Proteoform: a single term describing protein complexity.

Authors: Lloyd M Smith; Neil L Kelleher
Journal: Nat Methods Date: 2013-03 Impact factor: 28.547

3. Direct analysis of protein complexes using mass spectrometry.

Authors: A J Link; J Eng; D M Schieltz; E Carmack; G J Mize; D R Morris; B M Garvik; J R Yates
Journal: Nat Biotechnol Date: 1999-07 Impact factor: 54.908

4. 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

4 in total

11 in total

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

Authors: Hao Chi; Chao Liu; Hao Yang; Wen-Feng Zeng; Long Wu; Wen-Jing Zhou; Rui-Min Wang; Xiu-Nan Niu; Yue-He Ding; Yao Zhang; Zhao-Wei Wang; Zhen-Lin Chen; Rui-Xiang Sun; Tao Liu; Guang-Ming Tan; Meng-Qiu Dong; Ping Xu; Pei-Heng Zhang; Si-Min He
Journal: Nat Biotechnol Date: 2018-10-08 Impact factor: 54.908

2. Top-Down Analysis of Branched Proteins Using Mass Spectrometry.

Authors: Dapeng Chen; Fabio Gomes; Dulith Abeykoon; Betsegaw Lemma; Yan Wang; David Fushman; Catherine Fenselau
Journal: Anal Chem Date: 2018-03-07 Impact factor: 6.986

3. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors.

Authors: Assaf Kacen; Aaron Javitt; Matthias P Kramer; David Morgenstern; Tomer Tsaban; Merav D Shmueli; Guo Ci Teo; Felipe da Veiga Leprevost; Eilon Barnea; Fengchao Yu; Arie Admon; Lea Eisenbach; Yardena Samuels; Ora Schueler-Furman; Yishai Levin; Alexey I Nesvizhskii; Yifat Merbl
Journal: Nat Biotechnol Date: 2022-10-06 Impact factor: 68.164

4. Top-down characterization of endogenous protein complexes with native proteomics.

Authors: Owen S Skinner; Nicole A Haverland; Luca Fornelli; Rafael D Melani; Luis H F Do Vale; Henrique S Seckler; Peter F Doubleday; Luis F Schachner; Kristina Srzentić; Neil L Kelleher; Philip D Compton
Journal: Nat Chem Biol Date: 2017-11-13 Impact factor: 15.040

Illuminating the dark matter of shotgun proteomics.

1. Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics.

2. Proteoform: a single term describing protein complexity.

3. Direct analysis of protein complexes using mass spectrometry.

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

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

2. Top-Down Analysis of Branched Proteins Using Mass Spectrometry.

3. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors.

4. Top-down characterization of endogenous protein complexes with native proteomics.

5. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.

6. Focus on the spectra that matter by clustering of quantification data in shotgun proteomics.

7. TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets.

Review 8. A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field.

9. RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool.

10. Robust unsupervised deconvolution of linear motifs characterizes 68 protein modifications at proteome scale.