Chemical approaches for quantitative proteomics

Xiaobo focuses on developing novel isotope labeling-based tags for quantitative proteomics along two lines of research: (1) In data-dependent acquisition (DDA) mode, eliminating the ratio distortion caused by peptide cofragmentation and increasing the multiplexing capacity. (2) In data-independent acquisition (DIA) mode, achieving multiplexed quantification with general DIA LC-MS settings. The representative work, Ac-IP tag that specifically suitable for the multiplexing in DIA mode, attracted much attention from peers

Accurate and fast two-step phase shifting algorithm based on principle component analysis and Lissajous ellipse fitting with random phase shift and no pre-filtering

To achieve high measurement accuracy with less computational time-in-phase shifting interferometry, a random phase-shifting algorithm based on principal component analysis and Lissajous ellipse fitting (PCA& LEF) is proposed. It doesn't need pre-filtering and can obtain relatively accurate phase distribution with only two phase shifted interferograms and less computational time and is suitable for different background intensity, modulation amplitude distributions and noises. Moreover, it can obtain absolutely accurate result when the background intensity and modulation amplitude are perfect and can partly suppress the effect of imperfect background intensity and modulation amplitude. Last but not least, it removes the restriction that PCA needs more than three interferograms with welldistributed phase shifts to subtract relatively accurate mean. The simulations and experiments verify the correctness and feasibility of PCA& LEF. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing AgreementNational Natural Science Foundation of China (NSFC) [11304034]; Department of Science and Technology of Jilin Province [20190701018GH]; Education Department of Jilin Province [JJKH20190691KJ]; State Key Laboratory of Applied OpticsOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Multi-horseshoe dense property and intermediate entropy property of ergodic measures with same level

Katok conjectured that for every $C^{2}$ diffeomorphism $f$ on a Riemannian manifold $X$, the set $\{h_{\mu}(f):\mu \text{ is an ergodic measure for } (X,f)\}$ includes $[0, h_{top}(f))$. In this paper we obtained a refined Katok's conjecture on intermediate metric entropies of ergodic measures with same level that for a transitive locally maximal hyperbolic set or a transitive two-side subshit of finite type, one has $$\mathrm{Int}(\{h_{\mu}(f):\mu\in M_{erg}(f,X) \text{ and }\int\varphi d\mu=a\})=\mathrm{Int}(\{h_{\mu}(f):\mu\in M(f,X) \text{ and }\int\varphi d\mu=a\})$$ for any $a\in \left(\inf_{\mu\in M(f,X)}\int\varphi d\mu, \, \sup_{\mu\in M(f,X)}\int\varphi d\mu\right)$ and any continuous function $\varphi$. In this process, we establish 'multi-horseshoe' entropy-dense property and use it to get the goal combined with conditional variational principles

SYSTEM INCLUDING CONOSCOPE LENS FOR MEASURING POLARIZATION CHARACTERISTICS OF WIDE FIELD-OF-VIEW LENSES

A lens measurement system including 1) a light source, 2) a lens mounting support configured to hold a lens so that light emitted by the light source is incident on the lens, 3) a conoscope lens positioned to receive light refracted by the lens, and 4) a polarization camera positioned to receive light emitted from the conoscope lens

Phase unwrapping in optical metrology via denoised and convolutional segmentation networks

The interferometry technique is corn commonly used to obtain the phase information of an object in optical metrology. The obtained wrapped phase is subject to a 27 pi ambiguity. To remove the ambiguity and obtain the correct phase, phase unwrapping is essential. Conventional phase unwrapping approaches are time-consuming and noise sensitive. To address those issues, we propose a new approach, where we transfer the task of phase unwrapping into a multi-class classification problem and introduce an efficient segmentation network to identify classes. Moreover, a noise-to-noise denoised network is integrated to preprocess noisy wrapped phase. We have demonstrated the proposed method with simulated data and in a real interferometric system.China Scholarship Council (CSC) [201704910730]; National Science Foundation (NSF) [1455630]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode

[Image: see text] Data-independent acquisition (DIA) is an increasingly used approach for quantitative proteomics. However, most current isotope labeling strategies are not suitable for DIA as they lead to more complex MS2 spectra or severe ratio distortion. As a result, DIA suffers from a lower throughput than data-dependent acquisition (DDA) due to a lower level of multiplexing. Herein, we synthesized an isotopically labeled acetyl-isoleucine-proline (Ac-IP) tag for multiplexed quantification in DIA. Differentially labeled peptides have distinct precursor ions carrying the quantitative information but identical MS2 spectra since the isotopically labeled Ac-Ile part leaves as a neutral loss upon collision-induced dissociation, while fragmentation of the peptide backbone generates regular fragment ions for identification. The Ac-IP-labeled samples can be analyzed using general DIA liquid chromatography–mass spectrometry settings, and the data obtained can be processed with established approaches. Relative quantification requires deconvolution of the isotope envelope of the respective precursor ions. Suitability of the Ac-IP tag is demonstrated with a triplex-labeled yeast proteome spiked with bovine serum albumin that was mixed at 10:5:1 ratios, resulting in measured ratios of 9.7:5.3:1.1

A Collision-Induced Dissociation Cleavable Isobaric Tag for Peptide Fragment Ion-Based Quantification in Proteomics

Quantifying peptides based on unique peptide fragment ions avoids the issue of ratio distortion that is commonly observed for reporter ion-based quantification approaches. Herein, we present a collision-induced dissociation-cleavable, isobaric acetyl-isoleucine-proline-glycine (Ac-IPG) tag, which conserves the merits of quantifying peptides based on unique fragments while reducing the complexity of the b-ion series compared to conventional fragment ion-based quantification methods thus facilitating data processing. Multiplex labeling is based on selective N-terminal dimethylation followed by derivatization of the ε-amino group of the C-terminal Lys residue of LysC peptides with isobaric Ac-IPG tags having complementary isotope distributions on Pro-Gly and Ac-Ile. Upon fragmentation between Ile and Pro, the resulting y ions, with the neutral loss of Ac-Ile, can be distinguished between the different labeling channels based on different numbers of isotope labels on the Pro-Gly part and thus contain the information for relative quantification, while b ions of different labeling channels have the same m/z values. The proteome quantification capability of this method was demonstrated by triplex labeling of a yeast proteome spiked with bovine serum albumin (BSA) over a 10-fold dynamic range. With the yeast proteins as the background, BSA was detected at ratios of 1.14:5.06:9.78 when spiked at 1:5:10 ratios. The raw mass data is available on the ProteomeXchange with the identifier PXD 018790

A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes

Quantifying proteins based on peptide-coupled reporter ions is a multiplexed quantitative strategy in proteomics that alleviates the problem of ratio distortion caused by peptide cofragmentation, as commonly observed in other reporter-ion-based approaches, such as TMT and iTRAQ. Data-independent acquisition (DIA) is an attractive alternative to data-dependent acquisition (DDA) due to its better reproducibility. While multiplexed labeling is widely used in DDA, it is rarely used in DIA, presumably because current approaches lead to more complex MS2 spectra, severe ratio distortion, or to a reduction in quantification accuracy and precision. Herein, we present a versatile acetyl-alanine-glycine (Ac-AG) tag that conceals quantitative information in isobarically labeled peptides and reveals it upon tandem MS in the form of peptide-coupled reporter ions. Since the peptide-coupled reporter ion is precursor-specific while fragment ions of the peptide backbone originating from different labeling channels are identical, the Ac-AG tag is compatible with both DDA and DIA. By isolating the monoisotopic peak of the precursor ion in DDA, intensities of the peptide-coupled reporter ions represent the relative ratios between constituent samples, whereas in DIA, the ratio can be inferred after deconvoluting the peptide-coupled reporter ion isotopes. The proteome quantification capability of the Ac-AG tag was demonstrated by triplex labeling of a yeast proteome spiked with bovine serum albumin (BSA) over a 10-fold dynamic range. Within this complex proteomics background, BSA spiked at 1:5:10 ratios was detected at ratios of 1.00:4.87:10.13 in DDA and 1.16:5.20:9.64 in DIA