382 related articles for article (PubMed ID: 25631240)
1. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.
Deutsch EW; Mendoza L; Shteynberg D; Slagel J; Sun Z; Moritz RL
Proteomics Clin Appl; 2015 Aug; 9(7-8):745-54. PubMed ID: 25631240
[TBL] [Abstract][Full Text] [Related]
2. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.
Slagel J; Mendoza L; Shteynberg D; Deutsch EW; Moritz RL
Mol Cell Proteomics; 2015 Feb; 14(2):399-404. PubMed ID: 25418363
[TBL] [Abstract][Full Text] [Related]
3. Platforms and Pipelines for Proteomics Data Analysis and Management.
Codrea MC; Nahnsen S
Adv Exp Med Biol; 2016; 919():203-215. PubMed ID: 27975218
[TBL] [Abstract][Full Text] [Related]
4. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.
Deutsch EW; Mendoza L; Shteynberg DD; Hoopmann MR; Sun Z; Eng JK; Moritz RL
J Proteome Res; 2023 Feb; 22(2):615-624. PubMed ID: 36648445
[TBL] [Abstract][Full Text] [Related]
5. A Galaxy of informatics resources for MS-based proteomics.
Mehta S; Bernt M; Chambers M; Fahrner M; Föll MC; Gruening B; Horro C; Johnson JE; Loux V; Rajczewski AT; Schilling O; Vandenbrouck Y; Gustafsson OJR; Thang WCM; Hyde C; Price G; Jagtap PD; Griffin TJ
Expert Rev Proteomics; 2023; 20(11):251-266. PubMed ID: 37787106
[TBL] [Abstract][Full Text] [Related]
6. Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline.
Keller A; Shteynberg D
Methods Mol Biol; 2011; 694():169-89. PubMed ID: 21082435
[TBL] [Abstract][Full Text] [Related]
7. A guided tour of the Trans-Proteomic Pipeline.
Deutsch EW; Mendoza L; Shteynberg D; Farrah T; Lam H; Tasman N; Sun Z; Nilsson E; Pratt B; Prazen B; Eng JK; Martin DB; Nesvizhskii AI; Aebersold R
Proteomics; 2010 Mar; 10(6):1150-9. PubMed ID: 20101611
[TBL] [Abstract][Full Text] [Related]
8. Trans-proteomic pipeline: a pipeline for proteomic analysis.
Pedrioli PG
Methods Mol Biol; 2010; 604():213-38. PubMed ID: 20013374
[TBL] [Abstract][Full Text] [Related]
9. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
Perez-Riverol Y; Wang R; Hermjakob H; Müller M; Vesada V; Vizcaíno JA
Biochim Biophys Acta; 2014 Jan; 1844(1 Pt A):63-76. PubMed ID: 23467006
[TBL] [Abstract][Full Text] [Related]
10. nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows.
Allen C; Meinl R; Paez JS; Searle BC; Just S; Pino LK; Fondrie WE
J Proteome Res; 2023 Aug; 22(8):2743-2749. PubMed ID: 37417926
[TBL] [Abstract][Full Text] [Related]
11. multiplierz: an extensible API based desktop environment for proteomics data analysis.
Parikh JR; Askenazi M; Ficarro SB; Cashorali T; Webber JT; Blank NC; Zhang Y; Marto JA
BMC Bioinformatics; 2009 Oct; 10():364. PubMed ID: 19874609
[TBL] [Abstract][Full Text] [Related]
12. Mass Spectrometry-Based Protein Quantification.
Chen Y; Wang F; Xu F; Yang T
Adv Exp Med Biol; 2016; 919():255-279. PubMed ID: 27975224
[TBL] [Abstract][Full Text] [Related]
13. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data.
Kuenzi BM; Borne AL; Li J; Haura EB; Eschrich SA; Koomen JM; Rix U; Stewart PA
J Proteome Res; 2016 Dec; 15(12):4747-4754. PubMed ID: 27680298
[TBL] [Abstract][Full Text] [Related]
14. APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools.
Malm EK; Srivastava V; Sundqvist G; Bulone V
BMC Bioinformatics; 2014 Dec; 15(1):441. PubMed ID: 25547515
[TBL] [Abstract][Full Text] [Related]
15. Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.
Kumar D; Yadav AK; Jia X; Mulvenna J; Dash D
Mol Cell Proteomics; 2016 Jan; 15(1):329-39. PubMed ID: 26560066
[TBL] [Abstract][Full Text] [Related]
16. WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline.
Chen CT; Ko CL; Choong WK; Wang JH; Hsu WL; Sung TY
Anal Chem; 2019 Aug; 91(15):9403-9406. PubMed ID: 31305071
[TBL] [Abstract][Full Text] [Related]
17. MS-PyCloud: A Cloud Computing-Based Pipeline for Proteomic and Glycoproteomic Data Analyses.
Hu Y; Schnaubelt M; Chen L; Zhang B; Hoang T; Lih TM; Zhang Z; Zhang H
Anal Chem; 2024 Jun; 96(25):10145-10151. PubMed ID: 38869158
[TBL] [Abstract][Full Text] [Related]
18. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.
Brusniak MY; Kwok ST; Christiansen M; Campbell D; Reiter L; Picotti P; Kusebauch U; Ramos H; Deutsch EW; Chen J; Moritz RL; Aebersold R
BMC Bioinformatics; 2011 Mar; 12():78. PubMed ID: 21414234
[TBL] [Abstract][Full Text] [Related]
19. Bioinformatic Analysis to Investigate Metaproteome Composition Using Trans-Proteomic Pipeline.
He S; Ranganathan S
Curr Protoc; 2022 Jul; 2(7):e506. PubMed ID: 35862176
[TBL] [Abstract][Full Text] [Related]
20. StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.
Hoopmann MR; Winget JM; Mendoza L; Moritz RL
J Proteome Res; 2018 Mar; 17(3):1314-1320. PubMed ID: 29400476
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
