Abstract:
:As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Cheng CY,Tsai CF,Chen YJ,Sung TY,Hsu WLdoi
10.1021/pr301039bsubject
Has Abstractpub_date
2013-05-03 00:00:00pages
2305-10issue
5eissn
1535-3893issn
1535-3907journal_volume
12pub_type
杂志文章abstract::The development of plasma biomarkers has proven to be more challenging than initially anticipated. Many studies have reported lists of candidate proteins rather than validated candidate markers with an assigned performance to a specific clinical objective. Biomarker research necessitates a clear rational framework wit...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/pr1008515
更新日期:2011-01-07 00:00:00
abstract::Our recent study first demonstrated that human bone marrow mesenchymal stem cell (hBMSC) transplantation could prevent death from fulminant hepatic failure (FHF) in pigs. To further clarify the metabolic mechanism of hBMSC transplantation in FHF, the plasma collected from FHF pigs that received transplantation of hBMS...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr3002639
更新日期:2012-06-01 00:00:00
abstract::Populus tremula L. x P. alba L. (Populus x canescens (Aiton) Smith), clone INRA 717-1-B4, saplings were subjected to 120 ppb ozone exposure for 28 days. Chloroplasts were isolated, and the membrane proteins, solubilized using the detergent 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), were analyzed in a differen...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr1012009
更新日期:2011-07-01 00:00:00
abstract::Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00873
更新日期:2017-02-03 00:00:00
abstract::T lymphocytes mediate cellular and humoral defense against foreign bodies or autoantigens. An understanding of T-cell information processing furthers studies of the immunological response. We describe a large-scale phosphorylation analysis of primary T cells using a multidimensional separation strategy, involving prep...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800500r
更新日期:2008-12-01 00:00:00
abstract::Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. H...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500196b
更新日期:2014-12-05 00:00:00
abstract::Spontaneous equine recurrent uveitis (ERU) is an incurable autoimmune disease affecting the eye. Although retinal-autoantigen specific T-helper 1 cells have been demonstrated to trigger disease progression and relapses, the molecular processes leading to retinal degeneration and consequent blindness remain unknown. To...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060668y
更新日期:2007-06-01 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::Acute kidney injury (AKI) is a frequent complication after cardiopulmonary bypass, but early detection of postoperative AKI remains challenging. Protein biomarkers predict AKI excellently in homogeneous cohorts but are less reliable in patients suffering from various comorbidities. We employed nuclear magnetic resonan...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00219
更新日期:2015-07-02 00:00:00
abstract::The Baculoviral IAP repeat-containing protein 5 (BIRC5), also known as inhibitor of apoptosis protein survivin, is a member of the chromosomal passenger complex and a key player in mitosis. To investigate the function of BIRC5 in liver regeneration, we analyzed a hepatocyte-specific BIRC5-knockout mouse model using a ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr401188r
更新日期:2014-06-06 00:00:00
abstract::Tumor invasion defines the transition between tissue-restricted carcinomas, related to good outcome as optimal surgery becomes possible, and metastatic tumors associated with poor prognosis and a dramatic decrease in survival. In endometrial cancer, myometrial infiltration represents a determinant parameter highly val...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900390t
更新日期:2009-10-01 00:00:00
abstract::The nation-wide electronic health record database acts as an interoperable repository of health data obtained throughout citizen contacts with health care providers. This system improves accessibility for citizens and researchers to health data with the ability to assign context to disease development. In that system,...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr1007784
更新日期:2011-01-07 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::We used a peptidomic approach for the analysis of the low molecular weight proteome in rat pancreatic tissue extracts. The goal was to develop a method that allows identifying endogenous peptides produced in the pancreas in the course of acute pancreatitis. The workflow combines peptides enrichment by centrifugal ultr...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr1002627
更新日期:2010-09-03 00:00:00
abstract::By foliar fortification with selenite, selenium (Se)-enriched rice with a higher Se content and grain yield has been generated. However, the regulatory mechanisms of Se response in rice grains remain unknown; therefore, we carried out a comparative proteomics study in Se-enriched rice grains by using two approaches in...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300878y
更新日期:2013-02-01 00:00:00
abstract::The effects of increased intake of dietary fiber as either whole grain rye or as resistant starch compared to a typical low dietary fiber Western-style diet on the metabolomics responses were studied in gastrointestinal content and tissue, peripheral plasma, and urine using a multicompartmental nontargeted liquid chro...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00039
更新日期:2015-08-07 00:00:00
abstract::Pathogenic events in Alzheimer's disease are believed to involve an imbalance between the production and clearance of the neurotoxic 42 amino acid form of the beta-amyloid peptide (Abeta1-42). Although much is known about the production of Abeta1-42, many questions remain about its degradation. Here, we describe an op...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0703627
更新日期:2007-11-01 00:00:00
abstract::New mass-tagging reagents for quantitative proteomics measurements have been designed using solid phase peptide synthesis technology. The solid phase mass tags have been used to accurately measure the relative amounts of cysteine-containing peptides in model peptide mixtures as well as in mixtures of tryptic digests i...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr034081k
更新日期:2004-01-01 00:00:00
abstract::To cope with sudden changes in the external environment, the budding yeast Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 ki...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.0c00253
更新日期:2020-08-07 00:00:00
abstract::Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complex...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0602803
更新日期:2006-10-01 00:00:00
abstract::Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a mutation in the Huntingtin gene, where excessive (≥ 36) CAG repeats encode for glutamine expansion in the huntingtin protein. Research using mouse models and human pathological material has indicated dysfunctions in a myriad of s...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500649m
更新日期:2014-12-05 00:00:00
abstract::Cancers are initiated and developed from a small population of stem-like cells termed cancer stem cells (CSCs). There is heterogeneity among this CSC population that leads to multiple subpopulations with their own distinct biological features and protein expression. The protein expression and function may be impacted ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00824
更新日期:2017-02-03 00:00:00
abstract::Moving from macroscale preparative systems in proteomics to micro- and nanotechnologies offers researchers the ability to deeply profile smaller numbers of cells that are more likely to be encountered in clinical settings. Herein a recently developed microscale proteomic method, microdroplet processing in one pot for ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.0c00629
更新日期:2021-01-25 00:00:00
abstract::Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b01035
更新日期:2016-10-07 00:00:00
abstract::Mequindox is used as a veterinary antibiotic drug. As part of systematic investigations into mequindox as a veterinary medicine and its subsequent applications in food safety, we conducted the investigation to assess the metabolic response of mice to mequindox using metabonomics, which combines NMR metabolic profiles ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr2006457
更新日期:2011-11-04 00:00:00
abstract::The balance between comprehensively analyzing the proteome and using valuable mass spectrometry time is a genuine challenge in the field of proteomics. Multidimensional fractionation strategies have significantly increased proteome coverage, but often at the cost of increased mass analysis time, despite advances in ma...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00082
更新日期:2019-05-03 00:00:00
abstract::Vascular leakage is a hallmark of severe dengue infection. Although extensive studies have been conducted during the past several decades, the molecular mechanisms underlying vascular leakage in dengue shock syndrome (DSS) remain unclear. We thus performed a proteomics study to characterize responses in human endothel...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900060g
更新日期:2009-05-01 00:00:00
abstract::In this report, we describe an integrated fluidic platform composed of tandem affinity columns for the depletion of high-abundance proteins from human serum and on-line fractionation/concentration of medium- and low-abundance proteins by tandem immobilized metal-ion affinity chromatography (IMAC) columns and reversed ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900399q
更新日期:2009-10-01 00:00:00
abstract::Many pressing medical challenges, such as diagnosing disease, enhancing directed stem-cell differentiation, and classifying cancers, have long been hindered by limitations in our ability to quantify proteins in single cells. Mass spectrometry (MS) is poised to transcend these limitations by developing powerful methods...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/acs.jproteome.8b00257
更新日期:2018-08-03 00:00:00
abstract::Knowledge of the protein networks interacting with the amyloid precursor protein (APP) in vivo can shed light on the physiological function of APP. To date, most proteins interacting with the APP intracellular domain (AICD) have been identified by Yeast Two Hybrid screens which only detect direct interaction partners....
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300123g
更新日期:2012-08-03 00:00:00