119 related articles for article (PubMed ID: 35441674)
1. Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation.
Na S; Choi H; Paek E
Bioinformatics; 2022 May; 38(11):2980-2987. PubMed ID: 35441674
[TBL] [Abstract][Full Text] [Related]
2. Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra.
Shen J; Pagala VR; Breuer AM; Peng J; Bin Ma ; Wang X
J Proteome Res; 2018 Sep; 17(9):3325-3331. PubMed ID: 30096983
[TBL] [Abstract][Full Text] [Related]
3. Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry.
Martin DM; Nett IR; Vandermoere F; Barber JD; Morrice NA; Ferguson MA
Bioinformatics; 2010 Sep; 26(17):2153-9. PubMed ID: 20651112
[TBL] [Abstract][Full Text] [Related]
4. Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy.
Jiang X; Han G; Feng S; Jiang X; Ye M; Yao X; Zou H
J Proteome Res; 2008 Apr; 7(4):1640-9. PubMed ID: 18314942
[TBL] [Abstract][Full Text] [Related]
5. Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search.
Lu B; Ruse CI; Yates JR
J Proteome Res; 2008 Aug; 7(8):3628-34. PubMed ID: 18563924
[TBL] [Abstract][Full Text] [Related]
6. Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides.
Tsai CF; Smith JS; Krajewski K; Zhao R; Moghieb AM; Nicora CD; Xiong X; Moore RJ; Liu T; Smith RD; Jacobs JM; Rajagopal S; Shi T
Anal Chem; 2019 Sep; 91(18):11606-11613. PubMed ID: 31418558
[TBL] [Abstract][Full Text] [Related]
7. Benchmarking common quantification strategies for large-scale phosphoproteomics.
Hogrebe A; von Stechow L; Bekker-Jensen DB; Weinert BT; Kelstrup CD; Olsen JV
Nat Commun; 2018 Mar; 9(1):1045. PubMed ID: 29535314
[TBL] [Abstract][Full Text] [Related]
8. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics.
Lam H; Deutsch EW; Aebersold R
J Proteome Res; 2010 Jan; 9(1):605-10. PubMed ID: 19916561
[TBL] [Abstract][Full Text] [Related]
9. New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics.
Peng Y; Jain S; Li YF; Greguš M; Ivanov AR; Vitek O; Radivojac P
Bioinformatics; 2020 Dec; 36(Suppl_2):i745-i753. PubMed ID: 33381824
[TBL] [Abstract][Full Text] [Related]
10. Reverse and Random Decoy Methods for False Discovery Rate Estimation in High Mass Accuracy Peptide Spectral Library Searches.
Zhang Z; Burke M; Mirokhin YA; Tchekhovskoi DV; Markey SP; Yu W; Chaerkady R; Hess S; Stein SE
J Proteome Res; 2018 Feb; 17(2):846-857. PubMed ID: 29281288
[TBL] [Abstract][Full Text] [Related]
11. Automatic validation of phosphopeptide identifications from tandem mass spectra.
Lu B; Ruse C; Xu T; Park SK; Yates J
Anal Chem; 2007 Feb; 79(4):1301-10. PubMed ID: 17297928
[TBL] [Abstract][Full Text] [Related]
12. PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search.
Dorl S; Winkler S; Mechtler K; Dorfer V
J Proteome Res; 2018 Jan; 17(1):290-295. PubMed ID: 29057658
[TBL] [Abstract][Full Text] [Related]
13. Optimization of TripleTOF spectral simulation and library searching for confident localization of phosphorylation sites.
Takai A; Tsubosaka T; Hirano Y; Hayakawa N; Tani F; Haapaniemi P; Suni V; Imanishi SY
PLoS One; 2019; 14(12):e0225885. PubMed ID: 31790495
[TBL] [Abstract][Full Text] [Related]
14. An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates.
Ahrné E; Ohta Y; Nikitin F; Scherl A; Lisacek F; Müller M
Proteomics; 2011 Oct; 11(20):4085-95. PubMed ID: 21898822
[TBL] [Abstract][Full Text] [Related]
15. Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry.
Hsu CC; Xue L; Arrington JV; Wang P; Paez Paez JS; Zhou Y; Zhu JK; Tao WA
J Am Soc Mass Spectrom; 2017 Jun; 28(6):1127-1135. PubMed ID: 28283928
[TBL] [Abstract][Full Text] [Related]
16. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3.
Navarrete-Perea J; Yu Q; Gygi SP; Paulo JA
J Proteome Res; 2018 Jun; 17(6):2226-2236. PubMed ID: 29734811
[TBL] [Abstract][Full Text] [Related]
17. SimPhospho: a software tool enabling confident phosphosite assignment.
Suni V; Suomi T; Tsubosaka T; Imanishi SY; Elo LL; Corthals GL
Bioinformatics; 2018 Aug; 34(15):2690-2692. PubMed ID: 29596608
[TBL] [Abstract][Full Text] [Related]
18. Mass Spectrometry-Based Proteomics for Analysis of Hydrophilic Phosphopeptides.
Tsai CF; Smith JS; Eiger DS; Martin K; Liu T; Smith RD; Shi T; Rajagopal S; Jacobs JM
Methods Mol Biol; 2021; 2259():247-257. PubMed ID: 33687720
[TBL] [Abstract][Full Text] [Related]
19. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis.
Payne SH; Yau M; Smolka MB; Tanner S; Zhou H; Bafna V
J Proteome Res; 2008 Aug; 7(8):3373-81. PubMed ID: 18563926
[TBL] [Abstract][Full Text] [Related]
20. Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics.
Madej D; Wu L; Lam H
J Proteome Res; 2022 Feb; 21(2):339-348. PubMed ID: 34989576
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]