Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

2015 ◽  
Vol 8 (380) ◽  
pp. rs6-rs6 ◽  
Author(s):  
Benjamin L. Parker ◽  
Guang Yang ◽  
Sean J. Humphrey ◽  
Rima Chaudhuri ◽  
Xiuquan Ma ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Insulin Signaling ◽  
Data Independent Acquisition ◽  
Using Data

scholarly journals Proteomic comparison of osteoarthritic and reference human menisci using data-independent acquisition mass spectrometry

2020 ◽  
Vol 28 (8) ◽  
pp. 1092-1101
Author(s):  
E. Folkesson ◽  
A. Turkiewicz ◽  
N. Ali ◽  
M. Rydén ◽  
H.V. Hughes ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Independent Acquisition ◽  
Using Data

scholarly journals Proteomic characterization of the normal human medial meniscus body using data‐independent acquisition mass spectrometry

2020 ◽  
Vol 38 (8) ◽  
pp. 1735-1745 ◽  
Author(s):  
Elin Folkesson ◽  
Aleksandra Turkiewicz ◽  
Martin Rydén ◽  
Harini Velocity Hughes ◽  
Neserin Ali ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Medial Meniscus ◽  
Data Independent Acquisition ◽  
Normal Human ◽  
Using Data

scholarly journals Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry

2016 ◽  
Vol 12 (8) ◽  
pp. 2385-2388 ◽  
Author(s):  
Simone Sidoli ◽  
Rina Fujiwara ◽  
Katarzyna Kulej ◽  
Benjamin A. Garcia
Keyword(s):  
Mass Spectrometry ◽  
Data Independent Acquisition ◽  
Modified Peptides ◽  
Using Data

Data-independent acquisition (DIA) is here applied to determine unexplored phosphorylation events on isobarically modified peptides.

scholarly journals Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry

2015 ◽  
Vol 14 (8) ◽  
pp. 3252-3262 ◽  
Author(s):  
Kimberly A. Krautkramer ◽  
Lukas Reiter ◽  
John M. Denu ◽  
James A. Dowell
Keyword(s):  
Mass Spectrometry ◽  
Histone Modifications ◽  
Data Independent Acquisition ◽  
Using Data

Identification of Mature Atherosclerotic Plaque Proteome Signatures Using Data-Independent Acquisition Mass Spectrometry

2017 ◽  
Vol 17 (1) ◽  
pp. 164-176 ◽  
Author(s):  
Nicole Hansmeier ◽  
Josef Buttigieg ◽  
Pankaj Kumar ◽  
Shaneen Pelle ◽  
Kyoo Yoon Choi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Atherosclerotic Plaque ◽  
Data Independent Acquisition ◽  
Using Data

scholarly journals DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data

2021 ◽  
Author(s):  
Yang Young Lu ◽  
Jeff Bilmes ◽  
Ricard A Rodriguez-Mias ◽  
Judit Villén ◽  
William Stafford Noble
Keyword(s):  
Mass Spectrometry ◽  
Complex Structure ◽  
Mass Spectrometry Data ◽  
Peptide Sequence ◽  
Sequence Database ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Using Data ◽  
Tandem Mass Spectrometry Data ◽  
Analyze Data

AbstractTandem mass spectrometry data acquired using data independent acquisition (DIA) is challenging to interpret because the data exhibits complex structure along both the mass-to-charge (m/z) and time axes. The most common approach to analyzing this type of data makes use of a library of previously observed DIA data patterns (a “spectral library”), but this approach is expensive because the libraries do not typically generalize well across laboratories. Here we propose DIAmeter, a search engine that detects peptides in DIA data using only a peptide sequence database. Unlike other library-free DIA analysis methods, DIAmeter supports data generated using both wide and narrow isolation windows, can readily detect peptides containing post-translational modifications, can analyze data from a variety of instrument platforms, and is capable of detecting peptides even in the absence of detectable signal in the survey (MS1) scan.

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