| 1. |
- Brotons-Gisbert, Mauro, et al.
(author)
-
Out-of-plane orientation of luminescent excitons in two-dimensional indium selenide
- 2019
-
In: Nature Communications. - : Springer Nature. - 2041-1723. ; 10
-
Journal article (peer-reviewed)abstract
- Van der Waals materials offer a wide range of atomic layers with unique properties that can be easily combined to engineer novel electronic and photonic devices. A missing ingredient of the van der Waals platform is a two-dimensional crystal with naturally occurring out-of-plane luminescent dipole orientation. Here we measure the far-field photoluminescence intensity distribution of bulk InSe and two-dimensional InSe, WSe2 and MoSe2. We demonstrate, with the support of ab-initio calculations, that layered InSe flakes sustain luminescent excitons with an intrinsic out-of-plane orientation, in contrast with the in-plane orientation of dipoles we find in two-dimensional WSe2 and MoSe2 at room-temperature. These results, combined with the high tunability of the optical response and outstanding transport properties, position layered InSe as a promising semiconductor for novel optoelectronic devices, in particular for hybrid integrated photonic chips which exploit the out-of-plane dipole orientation.
|
|
| 2. |
- Eriksson, Jonatan O., et al.
(author)
-
MSIWarp : A General Approach to Mass Alignment in Mass Spectrometry Imaging
- 2020
-
In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 92:24, s. 16138-16148
-
Journal article (peer-reviewed)abstract
- Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (m/z) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free m/z alignment approach that is compatible with multiple instrument types and makes no assumptions on the sample's molecular composition. Our approach, MSIWarp (https://github.com/horvatovichlab/MSIWarp), finds an m/z recalibration function by maximizing a similarity score that considers both the intensity and m/z position of peaks matched between two spectra. MSIWarp requires only centroid spectra to find the recalibration function and is thereby readily applicable to almost any MSI data set. To deal with particularly misaligned or peak-sparse spectra, we provide an option to detect and exclude spurious peak matches with a tailored random sample consensus (RANSAC) procedure. We evaluate our approach with four publicly available data sets from both time-of-flight (TOF) and Orbitrap instruments and demonstrate up to 88% improvement in m/z alignment.
|
|
| 3. |
- Sánchez Brotons, Alejandro, et al.
(author)
-
Pipelines and Systems for Threshold-Avoiding Quantification of LC-MS/MS Data
- 2021
-
In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 93:32, s. 11215-11224
-
Journal article (peer-reviewed)abstract
- The accurate processing of complex liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) data from biological samples is a major challenge for metabolomics, proteomics, and related approaches. Here, we present the pipelines and systems for threshold-avoiding quantification (PASTAQ) LC-MS/MS preprocessing toolset, which allows highly accurate quantification of data-dependent acquisition LC-MS/MS datasets. PASTAQ performs compound quantification using single-stage (MS1) data and implements novel algorithms for high-performance and accurate quantification, retention time alignment, feature detection, and linking annotations from multiple identification engines. PASTAQ offers straightforward parameterization and automatic generation of quality control plots for data and preprocessing assessment. This design results in smaller variance when analyzing replicates of proteomes mixed with known ratios and allows the detection of peptides over a larger dynamic concentration range compared to widely used proteomics preprocessing tools. The performance of the pipeline is also demonstrated in a biological human serum dataset for the identification of gender-related proteins.
|
|
