| 1. |
- Berglund, Lisa, et al.
(författare)
-
A genecentric Human Protein Atlas for expression profiles based on antibodies
- 2008
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 7:10, s. 2019-2027
-
Forskningsöversikt (refereegranskat)abstract
- An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein toward all other human proteins. The new version is based on tissue profiles generated from 6120 antibodies with more than five million immunohistochemistry-based images covering 5067 human genes, corresponding to approximately 25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein-coupled receptors, etc., and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies has also been released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry, and, for a large fraction, immunofluorescence-based confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes, and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery.
|
|
| 2. |
- Skoeld, Karl, et al.
(författare)
-
The Impact of Biosampling Procedures on Molecular Data Interpretation
- 2013
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 12:6, s. 1489-1501
-
Forskningsöversikt (refereegranskat)abstract
- The separation between biological and technical variation without extensive use of technical replicates is often challenging, particularly in the context of different forms of protein and peptide modifications. Biosampling procedures in the research laboratory are easier to conduct within a shorter time frame and under controlled conditions as compared with clinical sampling, with the latter often having issues of reproducibility. But is the research laboratory biosampling really less variable? Biosampling introduces within minutes rapid tissue-specific changes in the cellular microenvironment, thus inducing a range of different pathways associated with cell survival. Biosampling involves hypoxia and, depending on the circumstances, hypothermia, circumstances for which there are evolutionarily conserved defense strategies in the range of species and also are relevant for the range of biomedical conditions. It remains unclear to what extent such adaptive processes are reflected in different biosampling procedures or how important they are for the definition of sample quality. Lately, an increasing number of comparative studies on different biosampling approaches, postmortem effects and pre-sampling biological state, have investigated such immediate early biosampling effects. Commonalities between biosampling effects and a range of ischemia/reperfusion- and hypometabolism/anoxia-associated biological phenomena indicate that even small variations in post-sampling time intervals are likely to introduce a set of nonrandom and tissue-specific effects of experimental importance (both in vivo and in vitro). This review integrates the information provided by these comparative studies and discusses how an adaptive biological perspective in biosampling procedures may be relevant for sample quality issues.
|
|
| 3. |
- Ting, Ying S., et al.
(författare)
-
Peptide-Centric Proteome Analysis : An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data
- 2015
-
Ingår i: Molecular & Cellular Proteomics. - : Elsevier BV. - 1535-9476 .- 1535-9484. ; 14:9, s. 2301-2307
-
Forskningsöversikt (refereegranskat)abstract
- In mass spectrometry-based bottom-up proteomics, data-independent acquisition is an emerging technique because of its comprehensive and unbiased sampling of precursor ions. However, current data-independent acquisition methods use wide precursor isolation windows, resulting in cofragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual tandem MS spectra are inherently limited in analyzing data-independent acquisition data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the unique characteristics of peptide-centric analysis in general.
|
|
| 4. |
- Uhlén, Mathias, et al.
(författare)
-
Antibody-based proteomics for human tissue profiling
- 2005
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:4, s. 384-393
-
Forskningsöversikt (refereegranskat)abstract
- Here, we describe the use of antibody-based proteomics involving the generation of protein-specific antibodies to functionally explore the human proteome. The antibodies can be used for analysis of corresponding proteins in a wide range of assay platforms, including i) immunohistochemistry for detailed tissue profiling, ii) specific affinity reagents for various functional protein assays, and iii) capture (pull-down) reagents for purification of specific proteins and their associated complexes for structural and biochemical analyses. In this review, the use of antibodies for such analysis will be discussed with focus on the possibility to create a descriptive and comprehensive protein atlas for tissue distribution and subcellular localization of human proteins in both normal and disease tissues.
|
|
| 5. |
- Zubarev, Roman, et al.
(författare)
-
On the proper use of mass accuracy in proteomics
- 2007
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 6:3, s. 377-381
-
Forskningsöversikt (refereegranskat)abstract
- Mass measurement is the main outcome of mass spectrometry-based proteomics yet the potential of recent advances in accurate mass measurements remains largely unexploited. There is not even a clear definition of mass accuracy in the proteomics literature, and we identify at least three uses of this term: anecdotal mass accuracy, statistical mass accuracy, and the maximum mass deviation (MMD) allowed in a database search. We suggest using the second of these terms as the generic one. To make the best use of the mass precision offered by modern instruments we propose a series of simple steps involving recalibration of the data on "internal standards" contained in every proteomics data set. Each data set should be accompanied by a plot of mass errors from which the appropriate MMD can be chosen. More advanced uses of high mass accuracy include an MMD that depends on the signal abundance of each peptide. Adapting search engines to high mass accuracy in the MS/MS data is also a high priority. Proper use of high mass accuracy data can make MS-based proteomics one of the most "digital" and accurate post-genomics disciplines.
|
|
| 6. |
- Barysz, Helena Maria, et al.
(författare)
-
Development of large-scale cross-linking mass spectrometry
- 2018
-
Ingår i: Molecular and Cellular Proteomics. - 1535-9484. ; 17:6, s. 1055-1066
-
Forskningsöversikt (refereegranskat)abstract
- Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level. Specifically, there is an unmet need for comprehensive software that can reliably identify cross-linked peptides from large datasets. In this review we provide supporting information to reason that targeted proteomics of cross-links may provide the required sensitivity to reliably detect and quantify cross-linked peptides and that a reporter ion signature for cross-linked peptides may become a useful approach to increase confidence in the identification process of cross-linked peptides. In addition, the review summarizes the recent advances in CLMS workflows using the analysis of condensin complex in intact chromosomes as a model complex.
|
|
