Literature DB >> 33091296

QuantPipe: A User-Friendly Pipeline Software Tool for DIA Data Analysis Based on the OpenSWATH-PyProphet-TRIC Workflow.

Dazheng Wang1, Guohong Gan1, Xi Chen2,3, Chuan-Qi Zhong1.   

Abstract

Targeted analysis of data-independent acquisition (DIA) mass spectrometry data requires elegant software tools and strict statistical control. OpenSWATH-PyProphet-TRIC is a widely used DIA data analysis workflow. The OpenSWATH-PyProphet-TRIC workflow is typically executed by running command lines. Here, we present QuantPipe, which is a graphic interface software tool based on the OpenSWATH-PyProphet-TRIC workflow. In addition to OpenSWATH-PyProphet-TRIC functions, QuantPipe can convert the spectral library to the assay library and output peptides and protein intensities. We demonstrated that QuantPipe can be used to analyze SWATH-MS data from TripleTOF 5600 and TripleTOF 6600, phospho-SWATH-MS data, DIA data from Orbitrap instrument, and diaPASEF data from TimsTOF Pro instrument. The executable files, user manual, and source code of QuantPipe are freely available at https://github.com/tachengxmu/QuantPipe/releases.

Entities:  

Keywords:  OpenSWATH; SWATH-MS; data-independent acquisition; diaPASEF

Mesh：

Year:  2020        PMID： 33091296     DOI： 10.1021/acs.jproteome.0c00704

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  5 in total

1.  Inner membrane complex proteomics reveals a palmitoylation regulation critical for intraerythrocytic development of malaria parasite.

Authors:  Pengge Qian; Xu Wang; Chuan-Qi Zhong; Jiaxu Wang; Mengya Cai; Wang Nguitragool; Jian Li; Huiting Cui; Jing Yuan
Journal:  Elife       Date:  2022-07-01       Impact factor: 8.713

2.  StackZDPD: a novel encoding scheme for mass spectrometry data optimized for speed and compression ratio.

Authors:  Jinyin Wang; Miaoshan Lu; Ruimin Wang; Shaowei An; Cong Xie; Changbin Yu
Journal:  Sci Rep       Date:  2022-03-30       Impact factor: 4.996

3.  Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time.

Authors:  Miaoshan Lu; Shaowei An; Ruimin Wang; Jinyin Wang; Changbin Yu
Journal:  BMC Bioinformatics       Date:  2022-01-12       Impact factor: 3.169

4.  Deep representation features from DreamDIAXMBD improve the analysis of data-independent acquisition proteomics.

Authors:  Mingxuan Gao; Wenxian Yang; Chenxin Li; Yuqing Chang; Yachen Liu; Qingzu He; Chuan-Qi Zhong; Jianwei Shuai; Rongshan Yu; Jiahuai Han
Journal:  Commun Biol       Date:  2021-10-14

5.  Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework.

Authors:  Matthias Fahrner; Melanie Christine Föll; Björn Andreas Grüning; Matthias Bernt; Hannes Röst; Oliver Schilling
Journal:  Gigascience       Date:  2022-02-15       Impact factor: 6.524
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.