Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics

Results from a combined test of an electromagnetic liquid argon calorimeter with a hadronic scintillating-tile calorimeter

The first combined test of an electromagnetic liquid argon accordion calorimeter and a hadronic scintillating-tile calorimeter was carried out at the CERN SPS. These devices are prototypes of the barrel calorimeter of the future ATLAS experiment at the LHC. The energy resolution of pions in the energy range from 20 to 300~GeV at an incident angle $\theta$ of about 11$^\circ$ is well-described by the expression \sigma/E = ((46.5 \pm 6.0)\%/\sqrt{E} +(1.2 \pm 0.3)\%) \oplus (3.2 \pm 0.4)~\mbox{GeV}/E. Shower profiles, shower leakage, and the angular resolution of hadronic showers were also studied

Test beam results of a stereo preshower integrated in the liquid argon accordion calorimeter

This paper describes the construction of an integrated preshower within the RD3 liquid argon accordion calorimeter. It has a stereo view which enables the measurement of two transverse coordinates. The prototype was tested at CERN with electrons, photons and muons to validate its capability to work at LHC ( Energy resolution, impact point resolution, angular resolution, $\pi^o$/$\gamma$ rejection )

Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants