Abstract：
:The localization of proteins at a tissue- or cell-type-specific level is tightly linked to the protein function. To better understand each protein's role in cellular systems, spatial information constitutes an important complement to quantitative data. The standard methods for determining the spatial distribution of proteins in single cells of complex tissue samples make use of antibodies. For a stringent analysis of the human proteome, we used orthogonal methods and independent antibodies to validate 5981 antibodies that show the expression of 3775 human proteins across all major human tissues. This enhanced validation uncovered 56 proteins corresponding to the group of "missing proteins" and 171 proteins of unknown function. The presented strategy will facilitate further discussions around criteria for evidence of protein existence based on immunohistochemistry and serves as a useful guide to identify candidate proteins for integrative studies with quantitative proteomics methods.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Sivertsson Å,Lindström E,Oksvold P,Katona B,Hikmet F,Vuu J,Gustavsson J,Sjöstedt E,von Feilitzen K,Kampf C,Schwenk JM,Uhlén M,Lindskog Cdoi
10.1021/acs.jproteome.0c00486subject
Has Abstractpub_date
2020-12-04 00:00:00pages
4766-4781issue
12eissn
1535-3893issn
1535-3907journal_volume
19pub_type
杂志文章abstract：:HER2-testing in breast and gastric cancers is mandatory for the treatment with trastuzumab. We hypothesized that imaging mass spectrometry (IMS) of breast cancers may be useful for generating a classifier that may determine HER2-status in other cancer entities irrespective of primary tumor site. A total of 107 breast ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100573s
更新日期：2010-12-03 00:00:00
abstract：:Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in reanalysis of public data sets, this experimental metadata may be missing or inaccurate. We descr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00954
更新日期：2019-04-05 00:00:00
abstract：:Eusocial behavior is extensively studied in the honeybee, Apis mellifera, as it displays an extreme form of altruism. Honeybee workers are generally obligatory sterile in a bee colony headed by a queen, but the inhibition of ovary activation is lifted upon the absence of queen and larvae. Worker bees are then able to ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201222s
更新日期：2012-05-04 00:00:00
abstract：:Trypanosoma cruzi is a protozoan that causes Chagas' disease, a neglected infectious illness that affects millions of people, mostly in Latin America. Here, the cell surface subproteome of the T. cruzi epimastigote life form was characterized. In order to prepare samples enriched in epimastigote plasma membrane protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400110h
更新日期：2013-07-05 00:00:00
abstract：:Cyanobacteria developed efficient carbon concentrating mechanisms which significantly improve the photosynthetic performance and survival of cells under limiting CO(2) conditions. Dynamic changes of the Synechocystis proteome to CO(2) limitation were investigated using shotgun LC-MS/MS approach with isobaric tag for r...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100651w
更新日期：2010-11-05 00:00:00
abstract：:In this study we selected three breast cancer cell lines (SKBR3, SUM149 and SUM190) with different oncogene expression levels involved in ERBB2 and EGFR signaling pathways as a model system for the evaluation of selective integration of subsets of transcriptomic and proteomic data. We assessed the oncogene status with...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4001527
更新日期：2013-06-07 00:00:00
abstract：:A fast and robust method for lipid profiling utilizing liquid chromatography coupled with mass spectrometry has been demonstrated and validated for the analysis of human plasma. This method allowed quantification and identification of lipids in human plasma using parallel alternating low energy and high energy collisi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr901094j
更新日期：2010-05-07 00:00:00
abstract：:Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400446z
更新日期：2013-12-06 00:00:00
abstract：:Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300953k
更新日期：2013-02-01 00:00:00
abstract：:The time course of the thylakoid membranes proteomic profile changes upon cadmium (Cd) addition to hydroponic Spinacia oleracea L. plants has been investigated. Two different proteomic approaches have been used: blue native gel electrophoresis followed by SDS-PAGE (2D BN-SDS-PAGE) and sucrose density gradient ultracen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800507x
更新日期：2009-01-01 00:00:00
abstract：:Hepatic fat export occurs by apolipoprotein B-100-containing lipoprotein production, whereas impaired production leads to liver steatosis. Hepatitis C virus (HCV) infection is associated to dysregulation of apoB-100 secretion and steatosis; however, the molecular mechanism by which HCV affects the apoB-100 secretion i...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201128s
更新日期：2012-05-04 00:00:00
abstract：:We have investigated whether postexercise ingestion of carbohydrates in combination with proteins generates a different systemic metabolic response, as compared to the sole ingestion of carbohydrate or water, in the early recovery phase following exercise. In addition, metabolic patterns related to fitness level were ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900081q
更新日期：2009-06-01 00:00:00
abstract：:Mixed lineage leukemia results from chromosomal rearrangements of the gene mixed lineage leukemia (MLL). MLL-AF9 is one such rearrangement that recruits the lysine methyltransferase, human disruptor of telomere silencing 1-like (DOT1L) and lysine specific demethylase 1 (LSD1), resulting in elevated expression of the H...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00118
更新日期：2018-08-03 00:00:00
abstract：:Epithelial cells play an important role in physiological and pathophysiological situations, with organ-, tissue-, type-, and function-specific patterns. Proteome analysis has been used to study epithelial-origin diseases and identify novel prognostic, diagnostic, and therapeutic markers. The present review compares th...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr050389v
更新日期：2006-04-01 00:00:00
abstract：:During the development of cancer, changes in cellular glycosylation are observed, indicating that alterations of the glycome occur in extracellular fluids as well as in serum and could therefore serve as tumor biomarkers. In the case of epithelial ovarian cancer (EOC), common tumor markers such as CA125 are known to h...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400405x
更新日期：2013-09-06 00:00:00
abstract：:Linear, short-chain polyfluorinated and perfluorinated alkyl compounds, often referred to as PFCs, have been in worldwide use as surfactants and polymer precursors for decades, and environmental dispersal of these highly persistent compounds represents a public health threat. Whereas ubiquitous low-level exposure to t...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr500990w
更新日期：2015-01-02 00:00:00
abstract：:The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunate...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800420s
更新日期：2008-10-01 00:00:00
abstract：:In this review, we lead the reader through the evolution of proteomics application to the study of quality control in production processes of foods (including food of plant origin and transgenic plants in particular, but also meat, wine and beer, and milk) and food safety (screening for foodborne pathogens). These top...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr2008829
更新日期：2012-01-01 00:00:00
abstract：:Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statis...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.9b00228
更新日期：2019-06-07 00:00:00
abstract：:Metal based chemotherapeutic drugs are widely used as an effective method to defeat various cancers. In this study, the mechanism of action of a novel therapeutic agent, [Pd(sac)(terpy)](sac)·4H2O (sac = saccharinate, and terpy = 2,2':6',2″-terpyridine) was studied. To better understand the proteomic changes in respon...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5006718
更新日期：2014-11-07 00:00:00
abstract：:The proteome of any system is a dynamic entity, such that the intracellular concentration of a protein is dictated by the relative rates of synthesis and degradation. In this work, we have analyzed time-dependent changes in the incorporation of a stable amino acid resolved precursor, a protocol we refer to as "dynamic...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800641v
更新日期：2009-01-01 00:00:00
abstract：:Numerous reports have predicted/hypothesized a role for probenazole-induced protein (PBZ1) as a molecular marker in rice self-defense mechanism. However, the precise function of PBZ1 remains unknown. In the present study, we examined PBZ1 as a putative cell death marker in rice. For this, we focused our attention on a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700878t
更新日期：2008-04-01 00:00:00
abstract：:In systemic amyloidosis, accumulation of misfolded proteins as extracellular amyloid fibrils in tissues causes severe organ dysfunction, but the molecular events of tissue damage related to amyloid deposition are still largely unknown. Through the use of the MudPIT proteomic approach, comprehensive protein profiles of...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400583h
更新日期：2013-12-06 00:00:00
abstract：:In this report, we use a proteomic strategy to identify glycoproteins on the surface of exosomes derived from myeloid-derived suppressor cells (MDSCs), and then test if selected glycoproteins contribute to exosome-mediated chemotaxis and migration of MDSCs. We report successful modification of a surface chemistry meth...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00811
更新日期：2017-01-06 00:00:00
abstract：:The current report describes the use of CapLC-ESI-Q/TOF-MS for investigating the proteome profiles of hypertonic saline-induced sputum samples from 56 smokers. The severity of their lung disease ranged from normal (healthy smokers) to chronic bronchitis, chronic obstructive pulmonary disease (COPD), and COPD with emph...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070440q
更新日期：2007-12-01 00:00:00
abstract：:Cooperia oncophora is one of the most common intestinal parasitic nematodes in cattle worldwide. To date, C. oncophora infections are treated using broad-spectrum anthelmintics. However, during the past decade, reports of anthelmintic resistance in this parasite species have emerged worldwide, necessitating new avenue...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400114y
更新日期：2013-09-06 00:00:00
abstract：:Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visuali...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b01031
更新日期：2016-07-01 00:00:00
abstract：:High-affinity antibodies binding to linear peptides in solution are a prerequisite for performing immuno-MRM, an emerging technology for protein quantitation with high precision and specificity using peptide immunoaffinity enrichment coupled to stable isotope dilution and targeted mass spectrometry. Recombinant antibo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4009404
更新日期：2014-04-04 00:00:00
abstract：:Dehydroeffusol (DHE) is a phenanthrene isolated from the Chinese medicinal plant Juncus effusus. Biological evaluation of DHE reveals in vitro and in vivo anticancer effects. We performed a shotgun proteomic analysis using liquid chromatography-tandem mass spectrometry to investigate the changes in the protein profile...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00227
更新日期：2018-07-06 00:00:00
abstract：:Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-reso...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200677z
更新日期：2012-02-03 00:00:00
