BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

331 related articles for article (PubMed ID: 25895889)

  • 1. Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra.
    Wang J; Zhang Y; Yu Y
    J Am Soc Mass Spectrom; 2015 Jul; 26(7):1077-84. PubMed ID: 25895889
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics.
    Amir SH; Yuswan MH; Aizat WM; Mansor MK; Desa MNM; Yusof YA; Song LK; Mustafa S
    J Proteomics; 2021 Jun; 241():104240. PubMed ID: 33894373
    [TBL] [Abstract][Full Text] [Related]  

  • 3. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.
    Audain E; Uszkoreit J; Sachsenberg T; Pfeuffer J; Liang X; Hermjakob H; Sanchez A; Eisenacher M; Reinert K; Tabb DL; Kohlbacher O; Perez-Riverol Y
    J Proteomics; 2017 Jan; 150():170-182. PubMed ID: 27498275
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data.
    Tu C; Sheng Q; Li J; Ma D; Shen X; Wang X; Shyr Y; Yi Z; Qu J
    J Proteome Res; 2015 Nov; 14(11):4662-73. PubMed ID: 26390080
    [TBL] [Abstract][Full Text] [Related]  

  • 5. BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics.
    Sheng Q; Dai J; Wu Y; Tang H; Zeng R
    J Proteome Res; 2012 Mar; 11(3):1494-502. PubMed ID: 22217156
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Two-dimensional target decoy strategy for shotgun proteomics.
    Bern MW; Kil YJ
    J Proteome Res; 2011 Dec; 10(12):5296-301. PubMed ID: 22010998
    [TBL] [Abstract][Full Text] [Related]  

  • 7. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.
    Kwon T; Choi H; Vogel C; Nesvizhskii AI; Marcotte EM
    J Proteome Res; 2011 Jul; 10(7):2949-58. PubMed ID: 21488652
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Search and decoy: the automatic identification of mass spectra.
    Eisenacher M; Kohl M; Turewicz M; Koch MH; Uszkoreit J; Stephan C
    Methods Mol Biol; 2012; 893():445-88. PubMed ID: 22665317
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Protein Identification from Tandem Mass Spectra by Database Searching.
    Edwards NJ
    Methods Mol Biol; 2017; 1558():357-380. PubMed ID: 28150247
    [TBL] [Abstract][Full Text] [Related]  

  • 10. PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.
    Edwards NJ
    Curr Protoc Bioinformatics; 2013 Dec; 44(1323):13.23.1-23. PubMed ID: 25663956
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Decoy methods for assessing false positives and false discovery rates in shotgun proteomics.
    Wang G; Wu WW; Zhang Z; Masilamani S; Shen RF
    Anal Chem; 2009 Jan; 81(1):146-59. PubMed ID: 19061407
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process.
    Feng XD; Li LW; Zhang JH; Zhu YP; Chang C; Shu KX; Ma J
    BMC Genomics; 2017 Mar; 18(Suppl 2):143. PubMed ID: 28361671
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Database Search Engines: Paradigms, Challenges and Solutions.
    Verheggen K; Martens L; Berven FS; Barsnes H; Vaudel M
    Adv Exp Med Biol; 2016; 919():147-156. PubMed ID: 27975215
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Faster SEQUEST searching for peptide identification from tandem mass spectra.
    Diament BJ; Noble WS
    J Proteome Res; 2011 Sep; 10(9):3871-9. PubMed ID: 21761931
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.
    Park GW; Hwang H; Kim KH; Lee JY; Lee HK; Park JY; Ji ES; Park SR; Yates JR; Kwon KH; Park YM; Lee HJ; Paik YK; Kim JY; Yoo JS
    J Proteome Res; 2016 Nov; 15(11):4082-4090. PubMed ID: 27537616
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Improving X!Tandem on peptide identification from mass spectrometry by self-boosted Percolator.
    Yang P; Ma J; Wang P; Zhu Y; Zhou BB; Yang YH
    IEEE/ACM Trans Comput Biol Bioinform; 2012; 9(5):1273-80. PubMed ID: 22689082
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.
    Tessier D; Lollier V; Larré C; Rogniaux H
    J Proteome Res; 2016 Oct; 15(10):3481-3488. PubMed ID: 27571036
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Quality assessments of peptide-spectrum matches in shotgun proteomics.
    Granholm V; Käll L
    Proteomics; 2011 Mar; 11(6):1086-93. PubMed ID: 21365749
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.
    Yu W; Taylor JA; Davis MT; Bonilla LE; Lee KA; Auger PL; Farnsworth CC; Welcher AA; Patterson SD
    Proteomics; 2010 Mar; 10(6):1172-89. PubMed ID: 20101609
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics.
    Madej D; Lam H
    J Proteome Res; 2023 Apr; 22(4):1159-1171. PubMed ID: 36962508
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 17.