Label-Free Quantification by Data Independent Acquisition Mass Spectrometry to Map Cardiovascular Proteomes

2016 ◽  
pp. 227-245
Author(s):  
Sarah J. Parker ◽  
Ronald J. Holewinski ◽  
Irina Tchernyshyov ◽  
Vidya Venkatraman ◽  
Laurie Parker ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Free Quantification

Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics

2016 ◽  
Vol 11 (4) ◽  
pp. 795-812 ◽  
Author(s):  
Ute Distler ◽  
Jörg Kuharev ◽  
Pedro Navarro ◽  
Stefan Tenzer
Keyword(s):  
Ion Mobility ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Free Quantification

scholarly journals Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC–MS/MS

2015 ◽  
Vol 14 (11) ◽  
pp. 4581-4593 ◽  
Author(s):  
Aivett Bilbao ◽  
Ying Zhang ◽  
Emmanuel Varesio ◽  
Jeremy Luban ◽  
Caterina Strambio-De-Castillia ◽  
...  
Keyword(s):  
Outlier Detection ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Fragment Ions ◽  
Free Quantification

scholarly journals Host defense responses of CO441 and CL30 maize lines to Fusarium graminearum analyzed by comparative label-free quantitative proteomics

2019 ◽  
Author(s):  
Lana M. Reid ◽  
Illimar Altosaar
Keyword(s):  
Mass Spectrometry ◽  
Fusarium Graminearum ◽  
Fungal Pathogen ◽  
Detailed Knowledge ◽  
Label Free ◽  
Maize Line ◽  
Defense Proteins ◽  
Label Free Quantification ◽  
Host Pathogen ◽  
Free Quantification

AbstractGibberella ear rot is a disease of maize associated with low yields and the production of harmful mycotoxins therein. The disease is caused by the infection of host Zea mays with fungal pathogen Fusarium graminearum. Resistant (CO441) and susceptible (CL30) inbred maize line kernels were inoculated with conidial suspensions of F. graminearum or water (controls). Ears of maize (cobs) from each line were harvested upon maturation and proteins were extracted from the embryo tissue of the kernels to study tissue-specific response of the host. Embryo proteins from both CO441 and CL30 lines were sequenced using mass spectrometry (LC-MS/MS) and quantified using Label Free Quantification (LFQ). Following filtering, 509 proteins were identified. These proteins were grouped into nine functional categories: Fusarium-derived, late embryogenesis abundant, oil-body, metabolism, stress, cellular, protein storage, metabolism, and defense. Defense proteins were up-regulated in response to infection in both CO441 and CL30 lines. Furthermore, F. graminearum derived proteins were only found in CL30 infected kernels suggesting that resistance may be attributed in part to the inability of Fusarium to establish itself in the embryo. To our knowledge this is the first successful application of LFQ mass spectrometry to the study of host-pathogen response to F. graminearum.Biological significanceFungal pathogen Fusarium graminearum is responsible for billion dollar losses in crops and contamination of global grains with harmful mycotoxins. By studying host-pathogen interactions of Fusarium and maize on a proteomic level with resistant and susceptible genotypes, the biological interactions occurring during infection of the maturing seed were characterized. Mature kernels of the F. graminearum susceptible maize line CL30 and resistant CO441 line were dissected to permit a proteomic survey of the new sporophytic generation, the embryo. Detailed knowledge of this Host-pathogen interactome will assist development of new cereal lines resistant to the rot diseases caused by Fusarium graminearum.HighlightsSusceptible (CL30) and Resistant (CO441) lines were injected with water mock or F. graminearum LC-MS/MS of maize embryo protein extracts followed by Label Free Quantification (LFQ) permitted identification, quantification and comparison of proteomes between maize genotypes and treatments Fusarium-derived proteins were abundant only in the susceptible infected embryo Defense proteomes were up-regulated in both lines following infection nsLTP and Protease Inhibitor were significantly over-expressed in the Susceptible line after infection; chitinase and WIP1 were significantly over-expressed in the Resistant line after infection

In-depth evaluation of software tools for data-independent acquisition based label-free quantification

PROTEOMICS ◽  
2015 ◽  
Vol 15 (18) ◽  
pp. 3140-3151 ◽  
Author(s):  
Jörg Kuharev ◽  
Pedro Navarro ◽  
Ute Distler ◽  
Olaf Jahn ◽  
Stefan Tenzer
Keyword(s):  
Software Tools ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Free Quantification

scholarly journals Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data

2013 ◽  
Vol 13 (1) ◽  
pp. 348-359 ◽  
Author(s):  
Erhan Kenar ◽  
Holger Franken ◽  
Sara Forcisi ◽  
Kilian Wörmann ◽  
Hans-Ulrich Häring ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Mass Spectrometry Data ◽  
Label Free ◽  
Liquid Chromatography Mass Spectrometry ◽  
Label Free Quantification ◽  
Chromatography Mass Spectrometry ◽  
Free Quantification
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