JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy

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JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1074/MCP.O114.039586
P932PMC publication ID4256513
P698PubMed publication ID25202125

P50authorYuxin LiQ55459198
P2093author name stringHong Wang
Junmin Peng
Xusheng Wang
Haiyan Tan
Zhiping Wu
P2860cites workA probability-based approach for high-throughput protein phosphorylation analysis and site localizationQ21735934
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysisQ24657366
Probability-based protein identification by searching sequence databases using mass spectrometry dataQ27860736
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseQ27861106
Mass spectrometry-based proteomicsQ28182890
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometryQ28209613
Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometryQ28284555
Open mass spectrometry search algorithmQ28286936
Error-tolerant identification of peptides in sequence databases by peptide sequence tagsQ28306769
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantificationQ29547200
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometryQ29547311
TANDEM: matching proteins with tandem mass spectraQ29615238
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteomeQ29615379
Andromeda: a peptide search engine integrated into the MaxQuant environmentQ29615816
Direct analysis of protein complexes using mass spectrometryQ29617450
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide IdentificationQ30053602
A statistical approach to peptide identification from clustered tandem mass spectrometry dataQ30653513
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databasesQ30882676
Analysis and validation of proteomic data generated by tandem mass spectrometryQ31131394
Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliabQ33216495
ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometerQ33224301
Development and validation of a spectral library searching method for peptide identification from MS/MS.Q33273391
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.Q33537380
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoringQ33607530
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessmentQ34118228
Computational and statistical analysis of protein mass spectrometry dataQ34145620
UniNovo: a universal tool for de novo peptide sequencingQ34350819
PepNovo: de novo peptide sequencing via probabilistic network modelingQ34414526
Sequence database searches via de novo peptide sequencing by tandem mass spectrometryQ34430804
NovoHMM: a hidden Markov model for de novo peptide sequencingQ34467135
False discovery rates in spectral identificationQ34486788
LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approachQ34897925
The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database searchQ35006588
Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies.Q35565880
A face in the crowd: recognizing peptides through database searchQ35579654
Rapid and reproducible single-stage phosphopeptide enrichment of complex peptide mixtures: application to general and phosphotyrosine-specific phosphoproteomics experimentsQ35650675
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the bookQ36079215
A proteomics search algorithm specifically designed for high-resolution tandem mass spectraQ36650680
Assigning significance to peptides identified by tandem mass spectrometry using decoy databasesQ37027478
Combining results of multiple search engines in proteomicsQ37160902
A HUPO test sample study reveals common problems in mass spectrometry-based proteomicsQ37447178
Systematical optimization of reverse-phase chromatography for shotgun proteomicsQ42068281
GutenTag: high-throughput sequence tagging via an empirically derived fragmentation modelQ42584462
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysisQ42663473
Editorial: from data to resultsQ42989382
Rapid and accurate peptide identification from tandem mass spectraQ43147563
The problem with peptide presumption and low Mascot scoringQ43423897
Semi-supervised learning for peptide identification from shotgun proteomics datasets.Q45965072
InsPecT: identification of posttranslationally modified peptides from tandem mass spectraQ46259455
pNovo: de novo peptide sequencing and identification using HCD spectraQ46533828
The coming age of complete, accurate, and ubiquitous proteomesQ86200825
P433issue12
P921main subjectdatabaseQ8513
search toolQ60461507
P304page(s)3663-3673
P577publication date2014-09-08
P1433published inMolecular & Cellular ProteomicsQ6895932
P1476titleJUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy
P478volume13

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cites work (P2860)
Q92314685A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice
Q68472501A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides
Q38611086Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data.
Q92264917Akt Phosphorylates NQO1 and Triggers its Degradation, Abolishing Its Antioxidative Activities in Parkinson's Disease
Q90408535Assessment and Refinement of Sample Preparation Methods for Deep and Quantitative Plant Proteome Profiling
Q33726445Autophagy, Endoplasmic Reticulum Stress and the Unfolded Protein Response in Intracerebral Hemorrhage
Q58710855BDNF inhibits neurodegenerative disease-associated asparaginyl endopeptidase activity via phosphorylation by AKT
Q47612203Binding of PLD2-Generated Phosphatidic Acid to KIF5B Promotes MT1-MMP Surface Trafficking and Lung Metastasis of Mouse Breast Cancer Cells
Q38701253Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.
Q101226760Combinatorial expression of GPCR isoforms affects signalling and drug responses
Q33719518Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry.
Q47234913Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Q92668705Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes
Q64104677Deep undepleted human serum proteome profiling toward biomarker discovery for Alzheimer's disease
Q91341516Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1
Q48108999Discrete roles and bifurcation of PTEN signaling and mTORC1-mediated anabolic metabolism underlie IL-7-driven B lymphopoiesis.
Q58745901ETV7 is an essential component of a rapamycin-insensitive mTOR complex in cancer
Q33787283Extensive Peptide Fractionation and y1 Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry.
Q38637167Informed-Proteomics: open-source software package for top-down proteomics.
Q50451267Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation.
Q37275719JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells
Q92614739LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity
Q92685482Metabolic switching in pluripotent stem cells reorganizes energy metabolism and subcellular organelles
Q36782739Multiple Weak Linear Motifs Enhance Recruitment and Processivity in SPOP-Mediated Substrate Ubiquitination
Q37482775PAX7 is a required target for microRNA-206-induced differentiation of fusion-negative rhabdomyosarcoma.
Q58611540Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a
Q50437928Quantitative Phosphoproteomic Analysis of Brain Tissues
Q56018329Quantitative phosphoproteomic analysis of the molecular substrates of sleep need
Q52691416SIL1, the endoplasmic-reticulum-localized BiP co-chaperone, plays a crucial role in maintaining skeletal muscle proteostasis and physiology.
Q36103911Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth
Q38601828The neoepitope landscape in pediatric cancers.
Q64356591ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97

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