4.3 Article

A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3

Wen-Feng Zeng et al.

Summary: The study introduces a new glycan-first glycopeptide search engine, pGlyco3, which can comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units, in a fast and accurate manner.

NATURE METHODS (2021)

Article Biochemical Research Methods

Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant

Andy Lin et al.

Summary: The standard proteomics database search strategy assumes all peptides in the database are relevant, but alternative strategies are needed when researchers are interested in a subset of peptides. Two recent methods failed to control the FDR, leading the authors to develop a new method (SNS) that considers neighbor peptides and outperforms existing methods in controlling the FDR.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biotechnology & Applied Microbiology

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

Hao Chi et al.

NATURE BIOTECHNOLOGY (2018)

Article Biotechnology & Applied Microbiology

Challenges and perspectives of metaproteomic data analysis

Robert Heyer et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Letter Biochemical Research Methods

Mass spectrometrists should search for all peptides, but assess only the ones they care about

Adriaan Sticker et al.

NATURE METHODS (2017)

Review Multidisciplinary Sciences

Mass-spectrometric exploration of proteome structure and function

Ruedi Aebersold et al.

NATURE (2016)

Article Biochemical Research Methods

Mass spectrometrists should search only for peptides they care about

William Stafford Noble

NATURE METHODS (2015)

Article Neurosciences

Cell type- and brain region-resolved mouse brain proteome

Kirti Sharma et al.

NATURE NEUROSCIENCE (2015)

Article Ecology

High-fat diet alters gut microbiota physiology in mice

Hannelore Daniel et al.

ISME JOURNAL (2014)

Review Biochemical Research Methods

Proteogenomics: concepts, applications and computational strategies

Alexey I. Nesvizhskii

NATURE METHODS (2014)

Article Multidisciplinary Sciences

MS-GF plus makes progress towards a universal database search tool for proteomics

Sangtae Kim et al.

NATURE COMMUNICATIONS (2014)

Review Chemistry, Multidisciplinary

Protein Analysis by Shotgun/Bottom-up Proteomics

Yaoyang Zhang et al.

CHEMICAL REVIEWS (2013)

Article Biochemical Research Methods

Comet: An open-source MS/MS sequence database search tool

Jimmy K. Eng et al.

PROTEOMICS (2013)

Article Engineering, Biomedical

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

John R. Yates et al.

Annual Review of Biomedical Engineering (2009)

Article Chemistry, Analytical

InsPecT: Identification of posttransiationally modified peptides from tandem mass spectra

S Tanner et al.

ANALYTICAL CHEMISTRY (2005)

Article Biochemical Research Methods

UniProt archive

R Leinonen et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

TANDEM: matching proteins with tandem mass spectra

R Craig et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

Unimod: Protein modifications for mass spectrometry

DM Creasy et al.

PROTEOMICS (2004)