Bottom-Up Shotgun Lipidomics by Higher Energy Collisional Dissociation on LTQ Orbitrap Mass Spectrometers

2011 ◽  
Vol 83 (14) ◽  
pp. 5480-5487 ◽  
Author(s):  
Kai Schuhmann ◽  
Ronny Herzog ◽  
Dominik Schwudke ◽  
Wolfgang Metelmann-Strupat ◽  
Stefan R. Bornstein ◽  
...  
Keyword(s):  
Shotgun Lipidomics ◽  
Bottom Up ◽  
Mass Spectrometers

scholarly journals Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics

2019 ◽  
Author(s):  
Yohann Couté ◽  
Christophe Bruley ◽  
Thomas Burger
Keyword(s):  
Mass Spectrometry ◽  
False Discovery Rate ◽  
Bottom Up ◽  
Mass Spectrometers ◽  
Popular Method ◽  
Protein Levels ◽  
False Discovery ◽  
Modern Mass

AbstractIn bottom-up discovery proteomics, target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control. Despite unquestionable statistical foundations, this method has drawbacks, including its hitherto unknown intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinter-preted. This article provides evidence that TDC has become less reliable as the accuracy of modern mass spectrometers improved. We therefore propose to replace TDC by a totally different method to control the FDR at spectrum, peptide and protein levels, while benefiting from the theoretical guarantees of the Benjamini-Hochberg framework. As this method is simpler to use, faster to compute and more stable than TDC, we argue that it is better adapted to the standardization and throughput constraints of current proteomic platforms.

scholarly journals Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics

2019 ◽  
Vol 91 (18) ◽  
pp. 12085-12093 ◽  
Author(s):  
Kai Schuhmann ◽  
HongKee Moon ◽  
Henrik Thomas ◽  
Jacobo Miranda Ackerman ◽  
Michael Groessl ◽  
...  
Keyword(s):  
Fragmentation Model ◽  
Shotgun Lipidomics ◽  
Bottom Up

scholarly journals EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification

2017 ◽  
Author(s):  
Sebastian Virreira Winter ◽  
Florian Meier ◽  
Christoph Wichmann ◽  
Juergen Cox ◽  
Matthias Mann ◽  
...  
Keyword(s):  
Collision Energy ◽  
Accurate Determination ◽  
High Yield ◽  
Bottom Up ◽  
Mass Spectrometers ◽  
New Generation

AbstractWe developed EASI-tag (Easily Abstractable Sulfoxide-based Isobaric tag), a new generation of amine-derivatizing and sulfoxide-containing isobaric labelling reagents, which dissociate at low collision energy and generate peptide-coupled, interference-free reporter ions with high yield. Efficient isolation of 12C precursors and quantification at the MS2 level enable accurate determination of quantitative differences between multiplexed samples. EASI-tag makes isobaric labeling applicable to any bottom up proteomics workflow and to benchtop mass spectrometers.

scholarly journals Shotgun Lipidomics on High Resolution Mass Spectrometers

2011 ◽  
Vol 3 (9) ◽  
pp. a004614-a004614 ◽  
Author(s):  
D. Schwudke ◽  
K. Schuhmann ◽  
R. Herzog ◽  
S. R. Bornstein ◽  
A. Shevchenko
Keyword(s):  
High Resolution ◽  
Shotgun Lipidomics ◽  
Mass Spectrometers ◽  
High Resolution Mass ◽  
Resolution Mass

Trial production of γ-type energy filtering TEM

1995 ◽  
Vol 53 ◽  
pp. 604-605
Author(s):  
Y. Taniguchi ◽  
E. Nakazawa ◽  
S. Taya
Keyword(s):  
Magnetic Energy ◽  
Electron Optics ◽  
Electron Microscopic ◽  
Mass Spectrometers ◽  
Ion Optics ◽  
Energy Filtering ◽  
New Information ◽  
New Type ◽  
Fringing Fields

Imaging energy filters can add new information to electron microscopic images with respect to energy-axis, so-called electron spectroscopic imaging (ESI). Recently, many good results have been reported using this imaging technique. ESI also allows high-contrast observation of unstained biological samples, becoming a trend of the field of morphology. We manufactured a new type of energy filter as a trial production. This energy filter consists of two magnets, and we call γ-filter since the trajectory of electrons shows ‘γ’-shape inside the filter. We evaluated the new energyγ-filter TEM with the γ-filter.Figure 1 shows schematic view of the electron optics of the γ-type energy filter. For the determination of the electron-optics of the γ-type energy filter, we used the TRIO (Third Order Ion Optics) program which has been developed for the design of high resolution mass spectrometers. The TRIO takes the extended fringing fields (EFF) into consideration. EFF makes it difficult to design magnetic energy filters with magnetic sector fields.

Psychology and Culture: Top Down Versus Bottom Up?

PsycCRITIQUES ◽  
2005 ◽  
Vol 50 (19) ◽  
Author(s):  
Michael Cole
Keyword(s):  
Top Down ◽  
Bottom Up
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