scholarly journals Generation of a mouse SWATH-MS spectral library to quantify 10148 proteins involved in cell reprogramming

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Uxue Ulanga ◽  
Matthew Russell ◽  
Stefano Patassini ◽  
Julie Brazzatti ◽  
Ciaren Graham ◽  
...  
Keyword(s):  
Stem Cell ◽  
Mass Spectra ◽  
Cell Reprogramming ◽  
Relative Quantification ◽  
Murine Models ◽  
Spectral Library ◽  
Reference Library ◽  
Data Independent Acquisition ◽  
Proteotypic Peptide ◽  
Novel Applications

AbstractMurine models are amongst the most widely used systems to study biology and pathology. Targeted quantitative proteomic analysis is a relatively new tool to interrogate such systems. Recently the need for relative quantification on hundreds to thousands of samples has driven the development of Data Independent Acquisition methods. One such technique is SWATH-MS, which in the main requires prior acquisition of mass spectra to generate an assay reference library. In stem cell research, it has been shown pluripotency can be induced starting with a fibroblast population. In so doing major changes in expressed proteins is inevitable. Here we have created a reference library to underpin such studies. This is inclusive of an extensively documented script to enable replication of library generation from the raw data. The documented script facilitates reuse of data and adaptation of the library to novel applications. The resulting library provides deep coverage of the mouse proteome. The library covers 29519 proteins (53% of the proteome) of which 7435 (13%) are supported by a proteotypic peptide.

scholarly journals Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition

2019 ◽  
Vol 19 (1) ◽  
pp. 181-197 ◽  
Author(s):  
Katalin Barkovits ◽  
Sandra Pacharra ◽  
Kathy Pfeiffer ◽  
Simone Steinbach ◽  
Martin Eisenacher ◽  
...  
Keyword(s):  
Relative Quantification ◽  
Spectral Library ◽  
Data Independent Acquisition

scholarly journals Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma

Metabolites ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 514
Author(s):  
Tom van der Laan ◽  
Isabelle Boom ◽  
Joshua Maliepaard ◽  
Anne-Charlotte Dubbelman ◽  
Amy C. Harms ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Mass Range ◽  
Correct Identification ◽  
Hydrophilic Interaction ◽  
Specific Mass ◽  
Structural Isomers ◽  
Data Independent Acquisition ◽  
Targeted Analysis ◽  
Theoretical Mass ◽  
Accurate Quantification

A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91–113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.

Generation of iPSCs from Genetically CorrectedBrca2Hypomorphic Cells: Implications in Cell Reprogramming and Stem Cell Therapy

Stem Cells ◽  
2014 ◽  
Vol 32 (2) ◽  
pp. 436-446 ◽  
Author(s):  
S. Navarro ◽  
V. Moleiro ◽  
F.J. Molina-Estevez ◽  
M.L. Lozano ◽  
R. Chinchon ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cell Therapy ◽  
Stem Cell Therapy ◽  
Cell Reprogramming

scholarly journals Review Paper: Implications of the “Cancer Stem Cell” Hypothesis on Murine Models of Colon Cancer and Colitis-associated Cancer

2009 ◽  
Vol 46 (5) ◽  
pp. 819-835 ◽  
Author(s):  
M. J. Hynes ◽  
K. M. Huang ◽  
E. H. Huang
Keyword(s):  
Colon Cancer ◽  
Stem Cell ◽  
Cancer Stem Cell ◽  
Murine Models ◽  
New Paradigm ◽  
Cancer Stem Cell Hypothesis ◽  
Molecular Events ◽  
Invaluable Tool ◽  
Relationship Of ◽  
The Relationship

The use of murine models to investigate human diseases has been an invaluable tool. In the areas of inflammation and oncogenesis, such models have provided unique insights into pathogenesis and mechanisms to evaluate potential therapy. As such, one facet of these disease processes links inflammation and cancer. Inflammation is associated with at least 15% of the world's malignancies. One example of this relationship is documented in the association between colitis and colorectal cancer. To date, the precise molecular events linking inflammation and cancer remain unclear. A new paradigm that may bridge these processes includes the cancer stem cell hypothesis. In this review, murine models of colitis, colon cancer, and colitis-associated cancer are discussed in reference to the potential of this paradigm to clarify the relationship of these devastating diseases.

Regenerative Chimerism Bioengineered Through Stem Cell Reprogramming

2013 ◽  
pp. 505-528
Author(s):  
Timothy J. Nelson ◽  
Almudena Martinez-Fernandez ◽  
Satsuki Yamada ◽  
Andre Terzic
Keyword(s):  
Stem Cell ◽  
Cell Reprogramming
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