| 1. |
- Brandsma, Corry Anke, et al.
(författare)
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Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1
- 2020
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Ingår i: Thorax. - : BMJ. - 0040-6376 .- 1468-3296. ; 75:2, s. 180-183
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Tidskriftsartikel (refereegranskat)abstract
- Translation of genomic alterations to protein changes in chronic obstructive pulmonary disease (COPD) is largely unexplored. Using integrated proteomic and RNA sequencing analysis of COPD and control lung tissues, we identified a protein signature in COPD characterised by extracellular matrix changes and a potential regulatory role for SUMO2. Furthermore, we identified 61 differentially expressed novel, non-reference, peptides in COPD compared with control lungs. This included two peptides encoding for a new splice variant of SORBS1, of which the transcript usage was higher in COPD compared with control lungs. These explorative findings and integrative proteogenomic approach open new avenues to further unravel the pathology of COPD.
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| 2. |
- Horvatovich, Péter, et al.
(författare)
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In vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins
- 2015
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3441-3451
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Tidskriftsartikel (refereegranskat)abstract
- Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered as “missing” proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these “missing” proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C–HPP teams (chromosomes 5, 10, 16 and 19) has joined forces to devise new strategies to identify “missing” proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low complexity samples derived from IVTT translation. The optimized assays are then applied to identify “missing” proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of eighteen “missing” proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
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| 3. |
- Horvatovich, Peter, et al.
(författare)
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Quest for Missing Proteins : Update 2015 on Chromosome-Centric Human Proteome Project
- 2015
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3415-3431
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wild (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.
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| 4. |
- Hägele, Martin, et al.
(författare)
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Industrial Robotics
- 2016
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Ingår i: Springer Handbooks. - Cham : Springer International Publishing. - 2522-8706 .- 2522-8692. ; , s. 1385-1422
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Bokkapitel (refereegranskat)abstract
- Much of the technology that makes robots reliable, human friendly, and industrialroboticsadaptable for numerous applications has emerged from manufacturers of industrial robots. With an estimated installation base in 2014 of about 1.5 million units, some 171000 new installations in that year and an annual turnover of the robotics industry estimated to be US$ 32 billion, industrial robots are by far the largest commercial application of robotics technology today. The foundations for robot motion planning and control were initially developed with industrial applications in mind. These applications deserve special attention in order to understand the origin of robotics science and to appreciate the many unsolved problems that still prevent the wider use of robots in today’s agile manufacturing agilemanufacturingenvironments. In this chapter, we present a brief history and descriptions of typical industrial robotics applications and at the same time we address current critical state-of-the-art technological developments. We show how robots with different mechanisms fit different applications and how applications are further enabled by latest technologies, often adopted from technological fields outside manufacturing automation. We will first present a brief historical introduction to industrial robotics with a selection of contemporary application examples which at the same time refer to a critical key technology. Then, the basic principles that are used in industrial robotics and a review of programming methods will be outlined. We will also introduce the topic of system integration particularly from a data integration point of view. The chapter will be closed with an outlook based on a presentation of some unsolved problems that currently inhibit wider use of industrial robots.
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| 5. |
- Nilsson, Klas, et al.
(författare)
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Productive Robots and the SMErobot Project
- 2005
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Ingår i: Book of Abstracts of Third Swedish Workshop on Autonomous Robotics.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The need for keeping manufacturing and workplacesin Europe calls for new ideas and concepts for productiverobots with focus on their usefulness for Small andMedium sized Enterprises (SMEs). The activitiesfrom the Robotics Research at LTH, [3], [4], [2], andin particular those related to the SMErobot project[1] comprise efforts in this direction. The SMErobotproject is a recently started four-year-project of the6th Framework Programme of the EC "to create anew family of SME-suitable robots and to exploit itspotentials for competitive SME manufacturing". Tothis purpose the goal is not to create fully autonomousrobots for all possible tasks, but rather to createsemi-autonomous robots and to allow for human-robotinteraction in a safe way.
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| 6. |
- Rosenling, Therese, et al.
(författare)
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Profiling and Identification of Cerebrospinal Fluid Proteins in a Rat EAE Model of Multiple Sclerosis.
- 2012
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Ingår i: Journal of Proteome Research. - 1535-3893 .- 1535-3907. ; 11:4, s. 2048-2060
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Tidskriftsartikel (refereegranskat)abstract
- The experimental autoimmune encephalomyelitis (EAE) model resembles certain aspects of multiple sclerosis (MScl), with common features such as motor dysfunction, axonal degradation, and infiltration of T-cells. We studied the cerebrospinal fluid (CSF) proteome in the EAE rat model to identify proteomic changes relevant for MScl disease pathology. EAE was induced in male Lewis rats by injection of myelin basic protein (MBP) together with complete Freund's adjuvant (CFA). An inflammatory control group was injected with CFA alone, and a nontreated group served as healthy control. CSF was collected at day 10 and 14 after immunization and analyzed by bottom-up proteomics on Orbitrap LC-MS and QTOF LC-MS platforms in two independent laboratories. By combining results, 44 proteins were discovered to be significantly increased in EAE animals compared to both control groups, 25 of which have not been mentioned in relation to the EAE model before. Lysozyme C1, fetuin B, T-kininogen, serum paraoxonase/arylesterase 1, glutathione peroxidase 3, complement C3, and afamin are among the proteins significantly elevated in this rat EAE model. Two proteins, afamin and complement C3, were validated in an independent sample set using quantitative selected reaction monitoring mass spectrometry. The molecular weights of the identified differentially abundant proteins indicated an increased transport across the blood-brain barrier (BBB) at the peak of the disease, caused by an increase in BBB permeability.
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| 7. |
- Rosenling, Therese, 1980-, et al.
(författare)
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The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF).
- 2009
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 8:12, s. 5511-22
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Tidskriftsartikel (refereegranskat)abstract
- To standardize the use of cerebrospinal fluid (CSF) for biomarker research, a set of stability studies have been performed on porcine samples to investigate the influence of common sample handling procedures on proteins, peptides, metabolites and free amino acids. This study focuses at the effect on proteins and peptides, analyzed by applying label-free quantitation using microfluidics nanoscale liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (chipLC-MS) as well as matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) and Orbitrap LC-MS/MS to trypsin-digested CSF samples. The factors assessed were a 30 or 120 min time delay at room temperature before storage at -80 degrees C after the collection of CSF in order to mimic potential delays in the clinic (delayed storage), storage at 4 degrees C after trypsin digestion to mimic the time that samples remain in the cooled autosampler of the analyzer, and repeated freeze-thaw cycles to mimic storage and handling procedures in the laboratory. The delayed storage factor was also analyzed by gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) for changes of metabolites and free amino acids, respectively. Our results show that repeated freeze/thawing introduced changes in transthyretin peptide levels. The trypsin digested samples left at 4 degrees C in the autosampler showed a time-dependent decrease of peak areas for peptides from prostaglandin D-synthase and serotransferrin. Delayed storage of CSF led to changes in prostaglandin D-synthase derived peptides as well as to increased levels of certain amino acids and metabolites. The changes of metabolites, amino acids and proteins in the delayed storage study appear to be related to remaining white blood cells. Our recommendations are to centrifuge CSF samples immediately after collection to remove white blood cells, aliquot, and then snap-freeze the supernatant in liquid nitrogen for storage at -80 degrees C. Preferably samples should not be left in the autosampler for more than 24 h and freeze/thaw cycles should be avoided if at all possible.
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| 8. |
- Rosenling, Therese, et al.
(författare)
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The experimental autoimmune encephalomyelitis model for proteomic biomarker studies : from rat to human.
- 2011
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Ingår i: Clinica Chimica Acta. - : Elsevier BV. - 0009-8981 .- 1873-3492. ; 412:11-12, s. 812-22
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Tidskriftsartikel (refereegranskat)abstract
- Multiple sclerosis (MScl) is defined by central nervous system (CNS) inflammation, demyelination and axonal damage. Some of the disease mechanisms are known but the cause of this complex disorder stays an enigma. Experimental autoimmune encephalomyelitis (EAE) is an animal model mimicking many aspects of MScl. This review aims to provide an overview over proteomic biomarker studies in the EAE model emphasizing the translational aspects with respect to MScl in humans.
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| 9. |
- Rosenling, Therese, et al.
(författare)
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The Impact of Delayed Storage on the Measured Proteome and Metabolome of Human Cerebrospinal Fluid
- 2011
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Ingår i: Clinical Chemistry. - : Oxford University Press (OUP). - 0009-9147 .- 1530-8561. ; 57:12, s. 1703-1711
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Because cerebrospinal fluid (CSF) is in close contact with diseased areas in neurological disorders, it is an important source of material in the search for molecular biomarkers. However, sample handling for CSF collected from patients in a clinical setting might not always be adequate for use in proteomics and metabolomics studies. METHODS: We left CSF for 0, 30, and 120 min at room temperature immediately after sample collection and centrifugation/removal of cells. After tryptic digestion at 2 laboratories by nanoLC Orbitrap-MS and chipLC QTOF-MS, CSF proteomes were analyzed. Metabolome analysis was performed at 3 laboratories by NMR, GC-MS, and LC-MS. Targeted analyses of cystatin C and albumin were performed by LC-MS/MS in the selected reaction monitoring mode. RESULTS: We did not find significant changes in the measured proteome and metabolome of CSF stored at room temperature after centrifugation, except for 2 peptides and 1 metabolite, 2,3,4-trihydrobutanoic acid, of 5780 identified peptides and 93 identified metabolites. A sensitive protein stability marker, cystatin C, was not affected. CONCLUSIONS: The measured proteome and metabolome of centrifuged, human CSF is stable at room temperature for up to 2 hours. We cannot exclude, however, that changes undetectable with our current methodology, such as denaturation or proteolysis, might occur due to sample handling conditions. The stability we observed gives laboratory personnel at the collection site sufficient time to aliquot samples before freezing and storage at -80 °C.
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| 10. |
- Sánchez Brotons, Alejandro, et al.
(författare)
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Pipelines and Systems for Threshold-Avoiding Quantification of LC-MS/MS Data
- 2021
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 93:32, s. 11215-11224
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Tidskriftsartikel (refereegranskat)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.
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