The proteomic future: where mass spectrometry should be taking us

High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

(2012) Joseph A Christie-Oleza et al.   BMC GENOMICS

Human Biomarker Discovery and Predictive Models for Disease Progression for Idiopathic Pneumonia Syndrome Following Allogeneic Stem Cell Transplantation

(2012) Daniela M. Schlatzer et al.   MOLECULAR & CELLULAR PROTEOMICS

Modification Site Localization Scoring: Strategies and Performance

(2012) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

Electron transfer dissociation mass spectrometry in proteomics

(2012) Min-Sik Kim et al.   PROTEOMICS

Biological signalling activity measurements using mass spectrometry

(2011) Pedro R. Cutillas et al.   BIOCHEMICAL JOURNAL

Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins

(2011) R. Shyama Prasad Rao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers

(2011) Mohammed Dakna et al.   BMC BIOINFORMATICS

Enhanced peptide quantification using spectral count clustering and cluster abundance

(2011) Seungmook Lee et al.   BMC BIOINFORMATICS

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics

(2011) Mohamed Helmy et al.   BMC PLANT BIOLOGY

Epigenetics: deciphering its role in diabetes and its chronic complications

(2011) Louisa M Villeneuve et al.   CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY

Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways

(2011) Hidetaka Kosako et al.   Expert Review of Proteomics

The discovery of novel protein-coding features in mouse genome based on mass spectrometry data

(2011) Xiao-Bin Xing et al.   GENOMICS

Comparison of Effect Sizes Associated With Biomarkers Reported in Highly Cited Individual Articles and in Subsequent Meta-analyses

(2011) John P. A. Ioannidis   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Analysis of Intact Protein Isoforms by Mass Spectrometry

(2011) Jeremiah D. Tipton et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The evolving field of imaging mass spectrometry and its impact on future biological research

(2011) Jeramie D. Watrous et al.   JOURNAL OF MASS SPECTROMETRY

NanoESI Mass Spectrometry of Rubisco and Rubisco Activase Structures and Their Interactions with Nucleotides and Sugar Phosphates

(2011) Michelle J. Blayney et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows

(2011) Emine Gokce et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Reflections on Charge State Distributions, Protein Structure, and the Mystical Mechanism of Electrospray Ionization

(2011) Omar M. Hamdy et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

An Alternative Paper Based Tissue Washing Method for Mass Spectrometry Imaging: Localized Washing and Fragile Tissue Analysis

(2011) Erika R. Amstalden van Hove et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The Future of Biological Mass Spectrometry

(2011) Marvin L. Vestal   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies

(2011) Michael Götze et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Accurate Quantification of Cardiovascular Biomarkers in Serum Using Protein Standard Absolute Quantification (PSAQ™) and Selected Reaction Monitoring

(2011) Céline Huillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Absolute Quantification of the Glycolytic Pathway in Yeast:

(2011) Kathleen M. Carroll et al.   MOLECULAR & CELLULAR PROTEOMICS

Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding

(2011) Elżbieta Lewandowska-Gnatowska et al.   PHYTOCHEMISTRY

Proteins of Diverse Function and Subcellular Location Are Lysine Acetylated in Arabidopsis

(2011) I. Finkemeier et al.   PLANT PHYSIOLOGY

Lysine Acetylation Is a Widespread Protein Modification for Diverse Proteins in Arabidopsis

(2011) X. Wu et al.   PLANT PHYSIOLOGY

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

(2011) Eli Venter et al.   PLoS One

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Improving Validation Practices in "Omics" Research

(2011) J. P. A. Ioannidis et al.   SCIENCE

The Three Musketeers of Autophagy: phosphorylation, ubiquitylation and acetylation

(2011) David G. McEwan et al.   TRENDS IN CELL BIOLOGY

MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets

(2011) Kristen M. Naegle et al.   PLoS Computational Biology

100% protein sequence coverage: a modern form of surrealism in proteomics

(2010) Bjoern Meyer et al.   AMINO ACIDS

Laser Desorption-Ionization of Lipid Transfers: Tissue Mass Spectrometry Imaging without MALDI Matrix

(2010) Veronika Vidová et al.   ANALYTICAL CHEMISTRY

MALDI-In Source Decay Applied to Mass Spectrometry Imaging: A New Tool for Protein Identification

(2010) Delphine Debois et al.   ANALYTICAL CHEMISTRY

Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics

(2010) Timothy S. Collier et al.   ANALYTICAL CHEMISTRY

Quantitation in Mass-Spectrometry-Based Proteomics

(2010) Waltraud X. Schulze et al.   Annual Review of Plant Biology

SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank

(2010) Willy Hugo et al.   BIOINFORMATICS

Towards clinical proteomics analysis

(2010) Kazuhiro Imai et al.   BIOMEDICAL CHROMATOGRAPHY

Nanotechniques in proteomics: Current status, promises and challenges

(2010) Sandipan Ray et al.   BIOSENSORS & BIOELECTRONICS

Emerging Analytical Separation Techniques with High Throughput Potential for Pharmaceutical Analysis, Part I: Stationary Phase and Instrumental Developments in LC

(2010) Sigrid Pieters et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Template-Based Protein Modeling: Recent Methodological Advances

(2010) Pankaj Daga et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Immobilized pH gradients

(2010) Elisabetta Gianazza et al.   ELECTROPHORESIS

Difference gel electrophoresis

(2010) Jonathan S. Minden et al.   ELECTROPHORESIS

Proteogenomics and systems biology: quest for the ultimate missing parts

(2010) Jean Armengaud   Expert Review of Proteomics

Identification of biomarkers for colorectal cancer through proteomics-based approaches

(2010) Harold Tjalsma   Expert Review of Proteomics

Isobaric protein and peptide quantification: perspectives and issues

(2010) Achim Treumann et al.   Expert Review of Proteomics

Mass spectrometry-based proteomics in biomedical research: emerging technologies and future strategies

(2010) Geraldine M. Walsh et al.   EXPERT REVIEWS IN MOLECULAR MEDICINE

Molecular mass spectrometry imaging in biomedical and life science research

(2010) Jaroslav Pól et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Mass microscopy: high-resolution imaging mass spectrometry

(2010) M. Setou et al.   Microscopy

A Multivariate Approach To Reveal Biomarker Signatures for Disease Classification: Application to Mass Spectral Profiles of Cerebrospinal Fluid from Patients with Multiple Sclerosis

(2010) Tarja Rajalahti et al.   JOURNAL OF PROTEOME RESEARCH

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

High-Throughput Middle-Down Analysis Using an Orbitrap

(2010) Joe Cannon et al.   JOURNAL OF PROTEOME RESEARCH

Quantitation of Soybean Allergens Using Tandem Mass Spectrometry

(2010) Norma L. Houston et al.   JOURNAL OF PROTEOME RESEARCH

Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry

(2010) James J. Moresco et al.   Journal of Proteomics

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

Seed proteomics

(2010) Ján A. Miernyk et al.   Journal of Proteomics

Integrating Lys-N proteolysis and N-terminal guanidination for improved fragmentation and relative quantification of singly-charged ions

(2010) Valerie J. Carabetta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

How far can we go with structural mass spectrometry of protein complexes?

(2010) Michal Sharon   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Monday posters

(2010)   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Developments and applications of mass microscopy

(2010) Mitsutoshi Setou et al.   Medical Molecular Morphology

Merging Molecular Electron Microscopy and Mass Spectrometry by Carbon Film-assisted Endoproteinase Digestion

(2010) Florian M. Richter et al.   MOLECULAR & CELLULAR PROTEOMICS

Sub-part-per-million Precursor and Product Mass Accuracy for High-throughput Proteomics on an Electron Transfer Dissociation-enabled Orbitrap Mass Spectrometer

(2010) Craig D. Wenger et al.   MOLECULAR & CELLULAR PROTEOMICS

Laserspray Ionization, a New Method for Protein Analysis Directly from Tissue at Atmospheric Pressure with Ultrahigh Mass Resolution and Electron Transfer Dissociation

(2010) Ellen D. Inutan et al.   MOLECULAR & CELLULAR PROTEOMICS

Megadalton Complexes in the Chloroplast Stroma ofArabidopsis thalianaCharacterized by Size Exclusion Chromatography, Mass Spectrometry, and Hierarchical Clustering

(2010) Paul Dominic B. Olinares et al.   MOLECULAR & CELLULAR PROTEOMICS

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins

(2010) Xiaowen Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Increased Power for the Analysis of Label-free LC-MS/MS Proteomics Data by Combining Spectral Counts and Peptide Peak Attributes

(2010) Lee Dicker et al.   MOLECULAR & CELLULAR PROTEOMICS

Profiling of Protein Interaction Networks of Protein Complexes Using Affinity Purification and Quantitative Mass Spectrometry

(2010) Robyn M. Kaake et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometry at the interface of proteomics and genomics

(2010) Karsten Krug et al.   Molecular BioSystems

Liposome-Based Chemical Barcodes for Single Molecule DNA Detection Using Imaging Mass Spectrometry

(2010) Anders Gunnarsson et al.   NANO LETTERS

Mass spectrometry in high-throughput proteomics: ready for the big time

(2010) Tommy Nilsson et al.   NATURE METHODS

Optimized localization analysis for single-molecule tracking and super-resolution microscopy

(2010) Kim I Mortensen et al.   NATURE METHODS

A bimolecular affinity purification method under denaturing conditions for rapid isolation of a ubiquitinated protein for mass spectrometry analysis

(2010) Gabriel N Maine et al.   Nature Protocols

Electrospray mass spectrometric investigation of the chaperone SecB

(2010) Virginia F. Smith et al.   PROTEIN SCIENCE

A gel-free quantitative proteomics approach to investigate temperature adaptation of the food-borne pathogen Cronobacter turicensis 3032

(2010) Paula Carranza et al.   PROTEOMICS

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Targeted large-scale analysis of protein acetylation

(2010) Nikolai Mischerikow et al.   PROTEOMICS

Multiplex assays for biomarker research and clinical application: Translational science coming of age

(2010) Qin Fu et al.   Proteomics Clinical Applications

Using proteomics to study sexual reproduction in angiosperms

(2010) Ján A. Miernyk et al.   SEXUAL PLANT REPRODUCTION

Post-translational modification by SUMO

(2010) Zara Hannoun et al.   TOXICOLOGY

Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling

(2010) Petras J. Kundrotas et al.   PLoS Computational Biology

Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques

(2009) J.L. Capelo et al.   ANALYTICA CHIMICA ACTA

Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures

(2009) Tonya Pekar Second et al.   ANALYTICAL CHEMISTRY

Nanostructure Initiator Mass Spectrometry: Tissue Imaging and Direct Biofluid Analysis

(2009) Oscar Yanes et al.   ANALYTICAL CHEMISTRY

The emerging complexity of protein ubiquitination

(2009) David Komander   BIOCHEMICAL SOCIETY TRANSACTIONS

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

(2009) Scott Bringans et al.   BMC BIOINFORMATICS

Ion mobility mass spectrometry of proteins and proteinassemblies

(2009) Charlotte Uetrecht et al.   CHEMICAL SOCIETY REVIEWS

A perfect genome annotation is within reach with the proteomics and genomics alliance

(2009) Jean Armengaud   CURRENT OPINION IN MICROBIOLOGY

Toward an atomic model of the 26S proteasome

(2009) Yifan Cheng   CURRENT OPINION IN STRUCTURAL BIOLOGY

New dimensions in the study of protein complexes using quantitative mass spectrometry

(2009) Silke Oeljeklaus et al.   FEBS LETTERS

Yeast Two-Hybrid, a Powerful Tool for Systems Biology

(2009) Anna Brückner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags

(2009) Loïc Dayon et al.   Journal of Proteomics

On-tissue protein identification and imaging by MALDI-Ion mobility mass spectrometry

(2009) Jonathan Stauber et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

What does the future hold for top down mass spectrometry?

(2009) Benjamin A. Garcia   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

(2009) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Predicting protein–protein interactions in the context of protein evolution

(2009) Anna C. F. Lewis et al.   Molecular BioSystems

Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks

(2009) S. Reiland et al.   PLANT PHYSIOLOGY

A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms

(2009) Chittibabu Guda et al.   PLoS One

A new generation of cross-linkers for selective detection by MALDI MS

(2009) David Paramelle et al.   PROTEOMICS

Sample preparation issues for tissue imaging by imaging MS

(2009) Başak Kükrer Kaletaş et al.   PROTEOMICS

Proteome analysis of Edwardsiella ictaluri

(2009) Pradeep R. Dumpala et al.   PROTEOMICS

Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse

(2009) Chang Jin Shin et al.   PROTEOMICS

Nanobiocatalysis for protein digestion in proteomic analysis

(2009) Jungbae Kim et al.   PROTEOMICS

Phosphopeptide enrichment with stable spatial coordination on a titanium dioxide coated glass slide

(2009) Susumu Y. Imanishi et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

On the high-resolution mass analysis of the product ions in tandem time-of-flight (TOF/TOF) mass spectrometers using a time-dependent re-acceleration technique

(2009) Sergey Kurnosenko et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Subunit Architecture of Multiprotein Assemblies Determined Using Restraints from Gas-Phase Measurements

(2009) Tara L. Pukala et al.   STRUCTURE

Phosphoproteomics

(2009) Nurhan Ozlu et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Mapping multiprotein complexes by affinity purification and mass spectrometry

(2008) Mark O Collins et al.   CURRENT OPINION IN BIOTECHNOLOGY

A practical interface for microfluidics and nanoelectrospray mass spectrometry

(2008) Sergio L. S. Freire et al.   ELECTROPHORESIS

Function and regulation of protein neddylation. ‘Protein Modifications: Beyond the Usual Suspects’ Review Series

(2008) Gwénaël Rabut et al.   EMBO REPORTS

Study of acetylation on Ser/Thr/Tyr/Lys, and trimethylation on Lys using electrospray tandem mass spectrometry

(2008) Yan Li et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

FT-ICR MS optimization for the analysis of intact proteins

(2008) Aleksey V. Tolmachev et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Regulatory Monoubiquitination of Phosphoenolpyruvate Carboxylase in Germinating Castor Oil Seeds

(2008) R. Glen Uhrig et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Combining Protein-Based IMAC, Peptide-Based IMAC, and MudPIT for Efficient Phosphoproteomic Analysis

(2008) Greg T. Cantin et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteome Analysis of Fission Yeast

(2008) Joshua T. Wilson-Grady et al.   JOURNAL OF PROTEOME RESEARCH

Strategy for Comprehensive Identification of Post-translational Modifications in Cellular Proteins, Including Low Abundant Modifications: Application to Glyceraldehyde-3-phosphate Dehydrogenase

(2008) Jawon Seo et al.   JOURNAL OF PROTEOME RESEARCH

Validation of gel-free, label-free quantitative proteomics approaches: Applications for seed allergen profiling

(2008) Severin E. Stevenson et al.   Journal of Proteomics

Enhancement of protein sensitivity for MALDI imaging mass spectrometry after chemical treatment of tissue sections

(2008) Erin H. Seeley et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Predicting Protein Post-translational Modifications Using Meta-analysis of Proteome Scale Data Sets

(2008) Daniel Schwartz et al.   MOLECULAR & CELLULAR PROTEOMICS

Visualizing the spatial distribution of secondary metabolites produced by marine cyanobacteria and sponges via MALDI-TOF imaging

(2008) Eduardo Esquenazi et al.   Molecular BioSystems

Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis

(2008) Naoyuki Sugiyama et al.   Molecular Systems Biology

Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis

(2008) Hin-Koon Woo et al.   Nature Protocols

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

(2008) Judit Villén et al.   Nature Protocols

P3DB: a plant protein phosphorylation database

(2008) J. Gao et al.   NUCLEIC ACIDS RESEARCH

Biochemical approaches for discovering protein-protein interactions

(2008) Jan A. Miernyk et al.   PLANT JOURNAL

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular imaging of proteins in tissues by mass spectrometry

(2008) E. H. Seeley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A nanostructure-initiator mass spectrometry-based enzyme activity assay

(2008) T. R. Northen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electrostatic Repulsion Hydrophilic Interaction Chromatography for Isocratic Separation of Charged Solutes and Selective Isolation of Phosphopeptides

(2007) Andrew J. Alpert   ANALYTICAL CHEMISTRY