Megavariate data analysis of mass spectrometric proteomics data using latent variable projection method

PROTEOMICS ◽  
2003 ◽  
Vol 3 (9) ◽  
pp. 1680-1686 ◽  
Author(s):  
Kwan R. Lee ◽  
Xiwu Lin ◽  
Daniel C. Park ◽  
Sergio Eslava
Keyword(s):  
Data Analysis ◽  
Projection Method ◽  
Latent Variable ◽  
Mass Spectrometric ◽  
Proteomics Data ◽  
Variable Projection

Application of Factor Analysis in Imaging Mass Spectrometric Data Analysis

2014 ◽  
Vol 42 (8) ◽  
pp. 1099-1103 ◽  
Author(s):  
Yi CHEN ◽  
Fei TANG ◽  
Tie-Gang LI ◽  
Jiu-Ming HE ◽  
Zeper ABLIZ ◽  
...  
Keyword(s):  
Factor Analysis ◽  
Data Analysis ◽  
Mass Spectrometric ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

A fourth-order auxiliary variable projection method for zero-Mach number gas dynamics

2008 ◽  
Vol 227 (3) ◽  
pp. 2012-2043 ◽  
Author(s):  
Samet Y. Kadioglu ◽  
Rupert Klein ◽  
Michael L. Minion
Keyword(s):  
Mach Number ◽  
Projection Method ◽  
Fourth Order ◽  
Gas Dynamics ◽  
Auxiliary Variable ◽  
Variable Projection

scholarly journals Comparison of TIMS-PASEF quantitative proteomics data-analysis workflows using FragPipe, DIA-NN, and Spectronaut from a user's perspective

2021 ◽  
Author(s):  
Alejandro Fernandez-Vega ◽  
Federica Farabegoli ◽  
Maria Mercedes Alonso-Martinez ◽  
Ignacio Ortea
Keyword(s):  
Data Analysis ◽  
Quantitative Proteomics ◽  
Real Life ◽  
Analysis Tool ◽  
Proteomics Data ◽  
Mass Spectrometers ◽  
Data Independent Acquisition ◽  
Proteomics Experiment ◽  
Under Sampling ◽  
The One

Data-independent acquisition (DIA) methods have gained great popularity in bottom-up quantitative proteomics, as they overcome the irreproducibility and under-sampling limitations of data-dependent acquisition (DDA). diaPASEF, recently developed for the timsTOF Pro mass spectrometers, has brought improvements to DIA, providing additional ion separation (in the ion mobility dimension) and increasing sensitivity. Several studies have benchmarked different workflows for DIA quantitative proteomics, but mostly using instruments from Sciex and Thermo, and therefore, the results are not extrapolable to diaPASEF data. In this work, using a real-life sample set like the one that can be found in any proteomics experiment, we compared the results of analyzing PASEF data with different combinations of library-based and library-free analysis, combining the tools of the FragPipe suite, DIA-NN and including MS1-level LFQ with DDA-PASEF data, and also comparing with the workflows possible in Spectronaut. We verified that library-independent workflows, not so efficient not so long ago, have greatly improved in the recent versions of the software tools, and now perform as well or even better than library-based ones. We report here information so that the user who is going to conduct a relative quantitative proteomics study using a timsTOF Pro mass spectrometer can make an informed decision on how to acquire (diaPASEF for DIA analysis, or DDA-PASEF for MS1-level LFQ) the samples, and what can be expected depending on the data analysis tool used, among the different alternatives offered by the recently optimized tools for TIMS-PASEF data analysis.

scholarly journals New Chromone, Isocoumarin, and Indole Alkaloid Derivatives from three Sponge-derived Fungal Strains

2016 ◽  
Vol 11 (9) ◽  
pp. 1934578X1601100 ◽  
Author(s):  
Ling-Hong Meng ◽  
Hui-Qin Chen ◽  
Imke Form ◽  
Belma Konuklugil ◽  
Peter Proksch ◽  
...  
Keyword(s):  
Data Analysis ◽  
Indole Alkaloid ◽  
Antimicrobial Activities ◽  
Fungal Strain ◽  
Mass Spectrometric ◽  
Mass Spectrometric Data ◽  
Spectrometric Data ◽  
Chromone Derivatives ◽  
Engyodontium Album ◽  
Ircinia Oros

Two new chromone derivatives, 2-hydroxymethyl-3-methyl-7-methoxychromone (1) and 2-hydroxymethyl-3- tert-butyl-7-methoxychromone (2), together with a related known compound, 2,3-dimethyl-7-methoxychromone (3), were isolated from Rhinocladiella sp. (IO2), a fungus obtained from the sponge Ircinia oros. Furthermore, a new isocoumarin derivative, 3-(3-chloro-2-hydroxypropyl)-8-hydroxy-6-methoxy-isochromen-1-one (4) and a known analogue 3-[( R)-3,3-dichloro-2-hydroxypropyl]-8-hydroxy-6-methoxy-1 H-isochromen-1-one (dichlorodiaportin, 5), were identified from sponge-derived fungal strain Clonostachys sp. (AP4.1), while a new indole alkaloid 1-(4-hydroxybenzoyl)indole-3-carbaldehyde (6) was obtained from the sponge-derived fungus Engyodontium album (IVB1b). The structures of these compounds were established by NMR spectroscopic and mass spectrometric data analysis, as well as by comparison with literature reports. Compounds 4 and 6 were examined for cytotoxic and antimicrobial activities, respectively. None of them showed potent activity.

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