Search results for "Quantitative proteomics"
showing 10 items of 29 documents
Label-Free Proteomics of Quantity-Limited Samples Using Ion Mobility-Assisted Data-Independent Acquisition Mass Spectrometry
2021
Over the past two decades, unbiased data-independent acquisition (DIA) approaches have gained increasing popularity in the bottom-up proteomics field. Here, we describe an ion mobility separation enhanced DIA workflow for large-scale label-free quantitative proteomics studies where starting material is limited. We set a special focus on the single pot solid-phase-enhanced sample preparation (SP3) protocol, which is well suited for the processing of quantity-limited samples.
Protein Quantitation: Lowry Protocol
2003
Protein quantitation according to the protocol of Lowry. Keywords: protein quantitation; lowry; folin–ciocalteu; calorimetric quantification
Automated analysis of images for molecular quantification in immunohistochemistry.
2018
The quantification of the expression of different molecules is a key question in both basic and applied sciences. While protein quantification through molecular techniques leads to the loss of spatial information and resolution, immunohistochemistry is usually associated with time-consuming image analysis and human bias. In addition, the scarce automatic software analysis is often proprietary and expensive and relies on a fixed threshold binarization. Here we describe and share a set of macros ready for automated fluorescence analysis of large batches of fixed tissue samples using FIJI/ImageJ. The quantification of the molecules of interest are based on an automatic threshold analysis of im…
The Complex Regulatory Role of Cytomegalovirus Nuclear Egress Protein pUL50 in the Production of Infectious Virus
2021
The regulation of the nucleocytoplasmic release of herpesviral capsids is defined by the process of nuclear egress. Due to their large size, nuclear capsids are unable to traverse via nuclear pores, so that herpesviruses evolved to develop a vesicular transport pathway mediating their transition through both leaflets of the nuclear membrane. This process involves regulatory proteins, which support the local distortion of the nuclear envelope. For human cytomegalovirus (HCMV), the nuclear egress complex (NEC) is determined by the pUL50-pUL53 core that initiates multicomponent assembly with NEC-associated proteins and capsids. Hereby, pUL50 serves as a multi-interacting determinant that recru…
The degradation of intracrystalline mollusc shell proteins: a proteomics study of Spondylus gaederopus.
2021
Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a "molecular clock" for geochronological applications. But despite seventy years of ancient protein research, the fundamental aspects of diagenesis-induced changes to protein structures and sequences remain elusive. In this study we investigate the degradation of intracrystalline proteins by performing artificial degradation experiments on the shell of the thorny oyster, Spo…
Peptides of the variable IgG domain as potential biomarker candidates in primary open-angle glaucoma (POAG)
2017
Autoantibody profiling has gained increasing interest in the research field of glaucoma promising the detection of highly specific and sensitive marker candidates for future diagnostic purposes. Recent studies demonstrated that immune responses are characterized by the expression of congruent or similar complementarity determining regions (CDR) in different individuals and could be used as molecular targets in biomarker discovery. Main objective of this study was to characterize glaucoma-specific peptides from the variable region of sera-derived immunoglobulins using liquid chromatography--mass spectrometry (LC-MS)-based quantitative proteomics. IgG was purified from sera of 13 primary open…
Data set of the protein expression profiles of Luminal A, Claudin-low and overexpressing HER2+ breast cancer cell lines by iTRAQ labelling and tandem…
2015
Breast cancer is the most common and the leading cause of mortality in women worldwide. There is a dire necessity of the identification of novel molecules useful in diagnosis and prognosis. In this work we determined the differentially expression profiles of four breast cancer cell lines compared to a control cell line. We identified 1020 polypeptides labelled with iTRAQ with more than 95% in confidence. We analysed the common proteins in all breast cancer cell lines through IPA software (IPA core and Biomarkers). In addition, we selected the specific overexpressed and subexpressed proteins of the different molecular classes of breast cancer cell lines, and classified them according to prot…
Data-independent acquisition strategies for quantitative proteomics
2013
In shotgun proteomics, data-dependent precursor acquisition (DDA) is widely used to profile protein components in complex samples. Although very popular, there are some inherent limitations to the DDA approach, such as irreproducible precursor ion selection, under-sampling and long instrument cycle times. Unbiased ‘data-independent acquisition’ (DIA) strategies try to overcome those limitations. In MSE, which is supported by Waters Q-TOF instrument platforms, such as the Synapt G2-S, a wide band pass filter is used for precursor selection. During acquisition, alternating MS scans are collected at low and high collision energy (CE), providing precursor and fragment ion information, respectiv…
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
2016
Nature Methods, 13 (9)
Protein content and lipid profiling of isolated native autophagosomes
2021
AbstractAutophagy is a central eukaryotic catabolic pathway responsible for clearance and recycling of an extensive portfolio of cargoes, which are packed in vesicles, called autophagosomes, and are delivered to lysosomes for degradation. Besides basal autophagy, which constantly degrades cellular material, the pathway is highly responsive to several stress conditions. However, the exact protein content and phospholipid composition of autophagosomes under changing autophagy conditions remain elusive so far. Here, we introduce a FACS-based approach for isolation of native unmanipulated autophagosomes and ensure the quality of the preparations. Employing quantitative proteomics and phospholip…