| Q37447178 | A HUPO test sample study reveals common problems in mass spectrometry-based proteomics |
| Q35579654 | A face in the crowd: recognizing peptides through database search |
| Q34728031 | A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics |
| Q33914424 | A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples |
| Q31109964 | A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data |
| Q42760054 | A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities |
| Q33361481 | A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time |
| Q34207316 | A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics |
| Q35348900 | Accurate assignment of significance to neuropeptide identifications using Monte Carlo k-permuted decoy databases |
| Q41894428 | Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies |
| Q28743720 | Advances in structure elucidation of small molecules using mass spectrometry |
| Q28569661 | Affinity pulldown of γ-secretase and associated proteins from human and rat brain |
| Q37945792 | Algorithms for the de novo sequencing of peptides from tandem mass spectra |
| Q33404909 | An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters |
| Q31029234 | An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64 |
| Q31131394 | Analysis and validation of proteomic data generated by tandem mass spectrometry |
| Q33415909 | Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data |
| Q37113889 | Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics |
| Q33305026 | Calibrating E-values for MS2 database search methods |
| Q33353663 | Challenges and solutions in proteomics |
| Q28550057 | Changes in the Proteome of Langat-Infected Ixodes scapularis ISE6 Cells: Metabolic Pathways Associated with Flavivirus Infection |
| Q46095722 | Chapter 8. Proteomic mapping of the vascular endothelium in vivo for vascular targeting |
| Q47140588 | Characterization of CobB kinetics and inhibition by nicotinamide. |
| Q34080008 | Characterization of glycoproteins in pancreatic cyst fluid using a high-performance multiple lectin affinity chromatography platform |
| Q38068929 | Chromosome-centric approach to overcoming bottlenecks in the Human Proteome Project |
| Q30987650 | Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics |
| Q37160902 | Combining results of multiple search engines in proteomics |
| Q33285992 | Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy |
| Q42120101 | Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. |
| Q36839627 | Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions |
| Q51770962 | Comparison of 1-D and 2-D LC MS/MS methods for proteomic analysis of human serum. |
| Q30000994 | Computational methods for protein identification from mass spectrometry data |
| Q36875645 | DNA Replication Stress Phosphoproteome Profiles Reveal Novel Functional Phosphorylation Sites on Xrs2 in Saccharomyces cerevisiae |
| Q33743194 | Data Management and Data Integration in the HUPO Plasma Proteome Project |
| Q41702227 | DeepPep: Deep proteome inference from peptide profiles. |
| Q47992332 | Discovery of gastric cancer specific biomarkers by the application of serum proteomics |
| Q34722654 | Dispec: a novel peptide scoring algorithm based on peptide matching discriminability |
| Q38089808 | Drug target identification and quantitative proteomics |
| Q33229418 | Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides |
| Q51926836 | EBP, a program for protein identification using multiple tandem mass spectrometry datasets. |
| Q33515901 | Elective affinities--bioinformatic analysis of proteomic mass spectrometry data |
| Q33530718 | Elucidation of the outer membrane proteome of Salmonella enterica serovar Typhimurium utilising a lipid-based protein immobilization technique |
| Q30429321 | Enhanced peptide quantification using spectral count clustering and cluster abundance |
| Q37212422 | Enhancing identifications of lipid-embedded proteins by mass spectrometry for improved mapping of endothelial plasma membranes in vivo |
| Q30486606 | Enhancing peptide identification confidence by combining search methods |
| Q30621030 | Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers |
| Q42396494 | Evaluation of database search programs for accurate detection of neuropeptides in tandem mass spectrometry experiments |
| Q33944444 | Evaluation of the Consensus of Four Peptide Identification Algorithms for Tandem Mass Spectrometry Based Proteomics. |
| Q37754062 | Existing bioinformatics tools for the quantitation of post-translational modifications |
| Q33915715 | Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation |
| Q35878790 | Generic comparison of protein inference engines |
| Q36689100 | Genome annotating proteomics pipelines: available tools |
| Q37698291 | Glycoprotein profiles of human breast cells demonstrate a clear clustering of normal/benign versus malignant cell lines and basal versus luminal cell lines |
| Q33262623 | Human body fluid proteome analysis |
| Q33957242 | Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms |
| Q43032658 | Identification of best indicators of peptide-spectrum match using a permutation resampling approach |
| Q33628868 | Identification of five candidate lung cancer biomarkers by proteomics analysis of conditioned media of four lung cancer cell lines |
| Q51124615 | Improved validation of peptide MS/MS assignments using spectral intensity prediction. |
| Q41822004 | Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines |
| Q41270109 | Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification |
| Q33688301 | Integrated data management and validation platform for phosphorylated tandem mass spectrometry data |
| Q35497551 | Integrated proteomic profiling of cell line conditioned media and pancreatic juice for the identification of pancreatic cancer biomarkers |
| Q33743189 | Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project’s Pilot Studies |
| Q27935768 | Intermembrane space proteome of yeast mitochondria |
| Q51820965 | Introducing the CPL/MUW proteome database: interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells. |
| Q51243711 | Investigation of scrambled ions in tandem mass spectra, part 2. On the influence of the ions on peptide identification. |
| Q34635037 | JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy |
| Q38089257 | Lost in translation: five grand challenges for proteomic biomarker discovery |
| Q31115628 | MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data |
| Q35083919 | MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines |
| Q33649026 | MacroSEQUEST: efficient candidate-centric searching and high-resolution correlation analysis for large-scale proteomics data sets |
| Q36375781 | Mapping the human plasma proteome by SCX-LC-IMS-MS |
| Q33249185 | Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1. |
| Q33411375 | MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data |
| Q43087698 | Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection |
| Q24648679 | Monte carlo simulation-based algorithms for analysis of shotgun proteomic data |
| Q36494331 | Neuroproteomics - the tasks lying ahead |
| Q30316302 | On the Extent of Tyrosine Phosphorylation in Chloroplasts. |
| Q35526306 | Ookinete-interacting proteins on the microvillar surface are partitioned into detergent resistant membranes of Anopheles gambiae midguts |
| Q21284208 | OpenMS - an open-source software framework for mass spectrometry |
| Q41669281 | Optimization of parameters for coverage of low molecular weight proteins |
| Q37065364 | Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems. |
| Q37358911 | Optimization of the Use of Consensus Methods for the Detection and Putative Identification of Peptides via Mass Spectrometry Using Protein Standard Mixtures |
| Q82591545 | Overview of Peptide and Protein Analysis by Mass Spectrometry |
| Q37144829 | Overview of tandem mass spectrometry (MS/MS) database search algorithms |
| Q30053602 | PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification |
| Q31118904 | Paleoproteomic study of the Iceman's brain tissue. |
| Q27972559 | Plasmodium falciparum AMA1 binds a rhoptry neck protein homologous to TgRON4, a component of the moving junction in Toxoplasma gondii |
| Q26999422 | Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments |
| Q42960165 | Practical and Efficient Searching in Proteomics: A Cross Engine Comparison |
| Q50053006 | Precursor ion independent algorithm for top-down shotgun proteomics |
| Q35690439 | ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity |
| Q48400535 | Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies |
| Q36805377 | Profiling and annotation of human kidney glomerulus proteome. |
| Q34013171 | Proteins modified by the lipid peroxidation aldehyde 9,12-dioxo-10(E)-dodecenoic acid in MCF7 breast cancer cells |
| Q37428856 | Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture. |
| Q34999444 | Proteome profiling of neuroblastoma-derived exosomes reveal the expression of proteins potentially involved in tumor progression |
| Q47318874 | Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night |
| Q39062013 | Proteomic analysis of the extracellular matrix produced by mesenchymal stromal cells: implications for cell therapy mechanism |
| Q38419611 | Proteomic analysis of three Borrelia burgdorferi sensu lato native species and disseminating clones: relevance for Lyme vaccine design |
| Q39491823 | Proteomic profiling of secretome and adherent plasma membranes from distinct mammary epithelial cell subpopulations. |
| Q37689362 | Proteomic research in psychiatry |
| Q33478412 | Proteomics Discovery of Disease Biomarkers |
| Q30601945 | Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies |
| Q38509974 | Proteomics identification and annotation of proteins of a cell line of Bombyx mori, BmN cells |
| Q34376138 | Proteomics of dense core secretory vesicles reveal distinct protein categories for secretion of neuroeffectors for cell-cell communication |
| Q34551808 | Proteomics profiling of Madin-Darby canine kidney plasma membranes reveals Wnt-5a involvement during oncogenic H-Ras/TGF-beta-mediated epithelial-mesenchymal transition |
| Q40295910 | Quantitative comparison of caste differences in honeybee hemolymph |
| Q46427445 | Quantitative peptidomics study reveals that a wound-induced peptide from PR-1 regulates immune signaling in tomato |
| Q30375585 | Quantitative proteomic analysis of histone modifications |
| Q34122195 | Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation |
| Q35963163 | Quantitative proteomics identifies surfactant-resistant alpha-synuclein in cerebral cortex of Parkinsonism-dementia complex of Guam but not Alzheimer's disease or progressive supranuclear palsy |
| Q24650980 | Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation |
| Q21203768 | RAId_DbS: peptide identification using database searches with realistic statistics |
| Q33639352 | Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry |
| Q50780129 | Report from the 2nd Annual US HUPO Meeting on the HUPO Human Plasma Proteome Project. |
| Q35589531 | RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids |
| Q30581490 | Searching for a needle in a stack of needles: challenges in metaproteomics data analysis |
| Q37154475 | Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry |
| Q39156915 | Sequence protein identification by randomized sequence database and transcriptome mass spectrometry (SPIDER-TMS): from manual to automatic application of a 'de novo sequencing' approach |
| Q24652437 | Shotgun proteomics in neuroscience |
| Q36833248 | Soluble nanopolymer-based phosphoproteomics for studying protein phosphatase |
| Q35217196 | Survivin is released from cancer cells via exosomes. |
| Q37397358 | Systems approach to explore components and interactions in the presynapse |
| Q57091959 | Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: Towards developing an MDCK protein database |
| Q33607513 | Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences |
| Q33631470 | Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses |
| Q40649350 | The Protein Acetyltransferase PatZ from Escherichia coli Is Regulated by Autoacetylation-induced Oligomerization |
| Q36218755 | The effect of peptide identification search algorithms on MS2-based label-free protein quantification |
| Q35047318 | The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput |
| Q36191416 | The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry |
| Q38010686 | The spectra count label-free quantitation in cancer proteomics. |
| Q36537397 | The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments |
| Q38847961 | TiO2 photocatalysis damages lipids and proteins in Escherichia coli |
| Q41997317 | Toward objective evaluation of proteomic algorithms |
| Q57091965 | Triton X-114 phase separation in the isolation and purification of mouse liver microsomal membrane proteins |
| Q42133439 | Use of biotinylated ubiquitin for analysis of rat brain mitochondrial proteome and interactome |
| Q37809187 | Utility, limitations, and promise of proteomics in animal science |
| Q33276082 | Validated MALDI-TOF/TOF mass spectra for protein standards |
| Q36661261 | Verification of single-peptide protein identifications by the application of complementary database search algorithms. |