scholarly journals Assessment of MS/MS Search Algorithms with Parent-Protein Profiling

2014 ◽  
Vol 13 (4) ◽  
pp. 1823-1832 ◽  
Author(s):  
Miin S. Lin ◽  
Justin J. Cherny ◽  
Claire T. Fournier ◽  
Samuel J. Roth ◽  
Danny Krizanc ◽  
...  
Keyword(s):  
Search Algorithms ◽  
Protein Profiling ◽  
Parent Protein ◽  
Ms Search

scholarly journals Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy

2007 ◽  
Vol 6 (9) ◽  
pp. 1599-1608 ◽  
Author(s):  
Brian M. Balgley ◽  
Tom Laudeman ◽  
Li Yang ◽  
Tao Song ◽  
Cheng S. Lee
Keyword(s):  
Comparative Evaluation ◽  
Search Strategy ◽  
Search Algorithms ◽  
Tandem Ms ◽  
Ms Search

scholarly journals An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

PROTEOMICS ◽  
2005 ◽  
Vol 5 (13) ◽  
pp. 3475-3490 ◽  
Author(s):  
Eugene A. Kapp ◽  
Frédéric Schütz ◽  
Lisa M. Connolly ◽  
John A. Chakel ◽  
Jose E. Meza ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Search Algorithms ◽  
Ms Search

scholarly journals An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

2006 ◽  
pp. 289-315
Author(s):  
Eugene A. Kapp ◽  
Frédéric Schütz ◽  
Lisa M. Connolly ◽  
John A. Chakel ◽  
Jose E. Meza ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Search Algorithms ◽  
Ms Search

Differentiation of Tumour from Normal Colorectal Tissue by SELDI-MS Protein Profiling

Endoscopy ◽  
2004 ◽  
Vol 36 (05) ◽  
Author(s):  
AM Lennon ◽  
D Stuart ◽  
AC Tan ◽  
E Fox ◽  
KS Sheahan ◽  
...  
Keyword(s):  
Protein Profiling ◽  
Colorectal Tissue ◽  
Normal Colorectal Tissue

Suzuki–Miyaura cross-coupling for chemoproteomic applications

2020 ◽  
Author(s):  
Jian Cao ◽  
Ernest Armenta ◽  
Lisa Boatner ◽  
Heta Desai ◽  
Neil Chan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cross Coupling ◽  
Protein Profiling ◽  
Protein Labeling ◽  
Caspase 8 ◽  
Complex Cell ◽  
Bioorthogonal Chemistry ◽  
Reaction Conditions ◽  
Target Deconvolution ◽  
Palladium Catalyzed

Bioorthogonal chemistry is a mainstay of chemoproteomic sample preparation workflows. While numerous transformations are now available, chemoproteomic studies still rely overwhelmingly on copper-catalyzed azide –alkyne cycloaddition (CuAAC) or 'click' chemistry. Here we demonstrate that gel-based activity-based protein profiling (ABPP) and mass-spectrometry-based chemoproteomic profiling can be conducted using Suzuki–Miyaura cross-coupling. We identify reaction conditions that proceed in complex cell lysates and find that Suzuki –Miyaura cross-coupling and CuAAC yield comparable chemoproteomic coverage. Importantly, Suzuki–Miyaura is also compatible with chemoproteomic target deconvolution, as demonstrated using structurally matched probes tailored to react with the cysteine protease caspase-8. Uniquely enabled by the observed orthogonality of palladium-catalyzed cross-coupling and CuAAC, we combine both reactions to achieve dual protein labeling.

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