Related references
Note: Only part of the references are listed.Applications of stable isotope dimethyl labeling in quantitative proteomics
Duangnapa Kovanich et al.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2012)
Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology
Juergen Cox et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 80 (2011)
More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC-MS/MS
Annette Michalski et al.
JOURNAL OF PROTEOME RESEARCH (2011)
Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos
Christian K. Frese et al.
JOURNAL OF PROTEOME RESEARCH (2011)
Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides
Salvatore Cappadona et al.
JOURNAL OF PROTEOMICS (2011)
Recent developments in quantitative proteomics
Christopher H. Becker et al.
MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS (2011)
Global quantification of mammalian gene expression control
Bjoern Schwanhaeusser et al.
NATURE (2011)
Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
Henry Lam et al.
METHODS (2011)
Discussion on common data analysis strategies used in MS-based proteomics
Rune Matthiesen et al.
PROTEOMICS (2011)
Generic workflow for quality assessment of quantitative label-free LC-MS analysis
Marianne Sandin et al.
PROTEOMICS (2011)
Less label, more free: Approaches in label-free quantitative mass spectrometry
Karlie A. Neilson et al.
PROTEOMICS (2011)
Accurate proteome-wide protein quantification from high-resolution N-15 mass spectra
Zia Khan et al.
GENOME BIOLOGY (2011)
Deconvolution of Mixture Spectra from Ion-Trap Data-Independent-Acquisition Tandem Mass Spectrometry
Marshall Bern et al.
ANALYTICAL CHEMISTRY (2010)
Quantitation in Mass-Spectrometry-Based Proteomics
Waltraud X. Schulze et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 61 (2010)
Methods for combining peptide intensities to estimate relative protein abundance
Brian Carrillo et al.
BIOINFORMATICS (2010)
Peek a peak: a glance at statistics for quantitative label-free proteomics
Katharina Podwojski et al.
EXPERT REVIEW OF PROTEOMICS (2010)
Role of spectral counting in quantitative proteomics
Deborah H. Lundgren et al.
EXPERT REVIEW OF PROTEOMICS (2010)
H-Score, a Mass Accuracy Driven Rescoring Approach for Improved Peptide Identification in Modification Rich Samples
Mikhail M. Savitski et al.
JOURNAL OF PROTEOME RESEARCH (2010)
Time Alignment Algorithms Based on Selected Mass Traces for Complex LC-MS Data
Christin Christin et al.
JOURNAL OF PROTEOME RESEARCH (2010)
Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics
Henry Lam et al.
JOURNAL OF PROTEOME RESEARCH (2010)
Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies
Stephane Houel et al.
JOURNAL OF PROTEOME RESEARCH (2010)
Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling in Diabetes Prone and Resistant Mice
Leo K. Iwai et al.
JOURNAL OF PROTEOME RESEARCH (2010)
MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics
Peter Mortensen et al.
JOURNAL OF PROTEOME RESEARCH (2010)
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
Alexey I. Nesvizhskii
JOURNAL OF PROTEOMICS (2010)
Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods
Jonas Grossmann et al.
JOURNAL OF PROTEOMICS (2010)
IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient Peptide Alignment Approach and Spectral Data Validation
Chih-Chiang Tsou et al.
MOLECULAR & CELLULAR PROTEOMICS (2010)
Comparative Assessment of Site Assignments in CID and Electron Transfer Dissociation Spectra of Phosphopeptides Discloses Limited Relocation of Phosphate Groups
Nikolai Mischerikow et al.
MOLECULAR & CELLULAR PROTEOMICS (2010)
Improving Software Performance for Peptide Electron Transfer Dissociation Data Analysis by Implementation of Charge State- and Sequence-Dependent Scoring
Peter R. Baker et al.
MOLECULAR & CELLULAR PROTEOMICS (2010)
Proteome-wide protein concentrations in the human heart
Thin Thin Aye et al.
MOLECULAR BIOSYSTEMS (2010)
The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput
John F. Kellie et al.
MOLECULAR BIOSYSTEMS (2010)
Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
Noelle M. Griffin et al.
NATURE BIOTECHNOLOGY (2010)
Enriching quantitative proteomics with SIN
Mihaela E. Sardiu et al.
NATURE BIOTECHNOLOGY (2010)
The pros and cons of peptide-centric proteomics
Mark W. Duncan et al.
NATURE BIOTECHNOLOGY (2010)
PeptideClassifier for protein inference and targeted quantitative proteomics
Ermir Qeli et al.
NATURE BIOTECHNOLOGY (2010)
De novo sequencing of peptides by MS/MS
Joerg Seidler et al.
PROTEOMICS (2010)
Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean
Alexandre Panchaud et al.
ANALYTICAL CHEMISTRY (2009)
UniMaP: finding unique mass and peptide signatures in the human proteome
Anastasia Alexandridou et al.
BIOINFORMATICS (2009)
StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry
Bas van Breukelen et al.
BIOINFORMATICS (2009)
Review of Peak Detection Algorithms in Liquid-Chromatography-Mass Spectrometry
Jianqiu Zhang et al.
CURRENT GENOMICS (2009)
Bioinformatics analysis of mass spectrometry-based proteomics data sets
Chanchal Kumar et al.
FEBS LETTERS (2009)
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
Monica A. Grobei et al.
GENOME RESEARCH (2009)
Quantitative mass spectrometry-based techniques for clinical use: Biomarker identification and quantification
Kathryn L. Simpson et al.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2009)
Quantification of Isotopically Overlapping Deamidated and 18O-Labeled Peptides Using Isotopic Envelope Mixture Modeling
Surendra Dasari et al.
JOURNAL OF PROTEOME RESEARCH (2009)
IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
Ze-Qiang Ma et al.
JOURNAL OF PROTEOME RESEARCH (2009)
iTRAQ Underestimation in Simple and Complex Mixtures: The Good, the Bad and the Ugly
Saw Yen Ow et al.
JOURNAL OF PROTEOME RESEARCH (2009)
A software program for more reliable precursor ion assignation from LC-MS analysis using LTQ ultra zoom scan
Takashi Shinkawa et al.
JOURNAL OF PROTEOMICS (2009)
Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications
David M. Good et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2009)
Development and Evaluation of Normalization Methods for Label-free Relative Quantification of Endogenous Peptides
Kim Kultima et al.
MOLECULAR & CELLULAR PROTEOMICS (2009)
Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling
Lily Ting et al.
MOLECULAR & CELLULAR PROTEOMICS (2009)
Comparative analysis to guide quality improvements in proteomics
Matthias Mann
NATURE METHODS (2009)
Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
Paul J. Boersema et al.
NATURE PROTOCOLS (2009)
Protein quantification across hundreds of experimental conditions
Zia Khan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
A comparison of MS/MS-based, stable-isotope-labeled, quantitation performance on ESI-quadrupole TOF and MALDI-TOF/TOF mass spectrometers
Michael A. Kuzyk et al.
PROTEOMICS (2009)
Interferences and contaminants encountered in modern mass spectrometry
Bernd O. Keller et al.
ANALYTICA CHIMICA ACTA (2008)
Exploring the precursor ion exclusion feature of liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry for improving protein identification in shotgun proteome analysis
Nan Wang et al.
ANALYTICAL CHEMISTRY (2008)
Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution μLC-MS data
Gregory L. Finney et al.
ANALYTICAL CHEMISTRY (2008)
Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer
Timothy S. Collier et al.
ANALYTICAL CHEMISTRY (2008)
Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomics
Joost W. Gouw et al.
ANALYTICAL CHEMISTRY (2008)
Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry
Salvatore Cappadona et al.
ANALYTICAL CHEMISTRY (2008)
Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications
Boris Macek et al.
Annual Review of Pharmacology and Toxicology (2008)
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Anoop M. Mayampurath et al.
BIOINFORMATICS (2008)
DAnTE: a statistical tool for quantitative analysis of -omics data
Ashoka D. Polpitiya et al.
BIOINFORMATICS (2008)
Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
Bryan A. P. Roxas et al.
BMC BIOINFORMATICS (2008)
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification
Magno Junqueira et al.
JOURNAL OF PROTEOME RESEARCH (2008)
The standard protein mix database: A diverse data set to assist in the production of improved peptide and protein identification software tools
John Klimek et al.
JOURNAL OF PROTEOME RESEARCH (2008)
Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: The comparison of two quantitative methods
Renata Usaite et al.
JOURNAL OF PROTEOME RESEARCH (2008)
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
Lukas N. Mueller et al.
JOURNAL OF PROTEOME RESEARCH (2008)
Robust and sensitive iTRAQ quantification on an LTQ orbitrap mass spectrometer
Marcus Bantscheff et al.
MOLECULAR & CELLULAR PROTEOMICS (2008)
In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types
Robert J. Chalkley et al.
MOLECULAR & CELLULAR PROTEOMICS (2008)
Selected reaction monitoring for quantitative proteomics: a tutorial
Vinzenz Lange et al.
MOLECULAR SYSTEMS BIOLOGY (2008)
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Juergen Cox et al.
NATURE BIOTECHNOLOGY (2008)
Decision tree-driven tandem mass spectrometry for shotgun proteomics
Danielle L. Swaney et al.
NATURE METHODS (2008)
Comparative LC-MS: A landscape of peaks and valleys
Antoine H. P. America et al.
PROTEOMICS (2008)
Alignment of LC-MS images, with applications to biomarker discovery and protein identification
Mathias Vandenbogaert et al.
PROTEOMICS (2008)
mzML: A single, unifying data format for mass spectrometer output
Eric Deutsch
PROTEOMICS (2008)
The properties of high-dimensional data spaces: implications for exploring gene and protein expression data
Robert Clarke et al.
NATURE REVIEWS CANCER (2008)
Top-down quantitation and characterization of SILAC-labeled proteins
Leonie F. Waanders et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2007)
Quantitative mass spectrometry in proteomics: a critical review
Marcus Bantscheff et al.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2007)
Quantitative profile of five murine core proteomes using label-free functional proteomics
Pedro R. Cutillas et al.
MOLECULAR & CELLULAR PROTEOMICS (2007)
Methods, algorithms and tools in computational proteomics: A practical point of view
Rune Matthiesen
PROTEOMICS (2007)
Reproducibility assessment of relative quantitation strategies for LC-MS based proteomics
Yeoun Jin Kim et al.
ANALYTICAL CHEMISTRY (2007)
Tools for computational processing of LC-MS datasets:: A user's perspective
Marius C. Codrea et al.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2007)
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
Alejandro Wolf-Yadlin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
Joshua E. Elias et al.
NATURE METHODS (2007)
An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics
Dennis Van Hoof et al.
NATURE METHODS (2007)
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
Peng Lu et al.
NATURE BIOTECHNOLOGY (2007)
eComputational prediction of proteotypic peptides for quantitative proteomics
Parag Mallick et al.
NATURE BIOTECHNOLOGY (2007)
Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach
Dirk Valkenborg et al.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2007)
A probability-based approach for high-throughput protein phosphorylation analysis and site localization
Sean A. Beausoleil et al.
NATURE BIOTECHNOLOGY (2006)
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
Boris Zybailov et al.
JOURNAL OF PROTEOME RESEARCH (2006)
Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS
Vitor Faca et al.
JOURNAL OF PROTEOME RESEARCH (2006)
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
K Flikka et al.
PROTEOMICS (2006)
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics
SJ Callister et al.
JOURNAL OF PROTEOME RESEARCH (2006)
Absolute quantification of proteins by LCMSE - A virtue of parallel MS acquisition
JC Silva et al.
MOLECULAR & CELLULAR PROTEOMICS (2006)
Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics
Erik L. Hendrickson et al.
ANALYST (2006)
Identification of post-translational modifications by blind search of mass spectra
D Tsur et al.
NATURE BIOTECHNOLOGY (2005)
Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap
JV Olsen et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
i-Tracker:: For quantitative proteomics using iTRAQ™ -: art. no. 145
IP Shadforth et al.
BMC GENOMICS (2005)
Comparison of label-free methods for quantifying human proteins by shotgun proteomics
WM Old et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
Mass spectrometry-based proteomics turns quantitative
SE Ong et al.
NATURE CHEMICAL BIOLOGY (2005)
Interpretation of shotgun proteomic data - The protein inference problem
AI Nesvizhskii et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
Y Ishihama et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
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 reliable and comprehensive automatic analysis of large datasets
RJ Chalkley et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra
DL Tabb et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2005)
Quantification of gel-separated proteins and their phosphorylation sites by LC-MS using unlabeled internal standards - Analysis of phosphoprotein dynamics in a B cell lymphoma cell line
PR Cutillas et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS
CJ Ji et al.
JOURNAL OF PROTEOME RESEARCH (2005)
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
J Listgarten et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS
H Steen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway
A Gruhler et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
Quantification in proteomics through stable isotope coding: A review
S Julka et al.
JOURNAL OF PROTEOME RESEARCH (2004)
Improving large-scale proteomics by clustering of mass spectrometry data
I Beer et al.
PROTEOMICS (2004)
Mass spectrometry-based quantitative proteomics
AJR Heck et al.
EXPERT REVIEW OF PROTEOMICS (2004)
DBParser: Web-based software for shotgun proteomic data analyses
XY Yang et al.
JOURNAL OF PROTEOME RESEARCH (2004)
The ABC's (and XYZ's) of peptide sequencing
H Steen et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2004)
Current chemical tagging strategies for proteome analysis by mass spectrometry
A Leitner et al.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2004)
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
HB Liu et al.
ANALYTICAL CHEMISTRY (2004)
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
PL Ross et al.
MOLECULAR & CELLULAR PROTEOMICS (2004)
Protein identification by mass spectrometry - Issues to be considered
MA Baldwin
MOLECULAR & CELLULAR PROTEOMICS (2004)
Deconvolution of isobaric interferences in mass spectra
J Meija et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2004)
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
MJ MacCoss et al.
ANALYTICAL CHEMISTRY (2003)
A universal denoising and peak picking algorithm for LC-MS based on matched filtration in the chromatographic time domain
VP Andreev et al.
ANALYTICAL CHEMISTRY (2003)
A statistical model for identifying proteins by tandem mass spectrometry
AI Nesvizhskii et al.
ANALYTICAL CHEMISTRY (2003)
Ion suppression in mass spectrometry
TM Annesley
CLINICAL CHEMISTRY (2003)
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
SA Gerber et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Tandem mass tags:: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
A Thompson et al.
ANALYTICAL CHEMISTRY (2003)
Mass spectrometry-based proteomics
R Aebersold et al.
NATURE (2003)
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
B Ma et al.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2003)
Initial implementation, of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control
ME Belov et al.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2003)
Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
D Chelius et al.
JOURNAL OF PROTEOME RESEARCH (2002)
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
SE Ong et al.
MOLECULAR & CELLULAR PROTEOMICS (2002)
Qscore: An algorithm for evaluating SEQUEST database search results
RE Moore et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2002)
DTASelect and contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
DL Tabb et al.
JOURNAL OF PROTEOME RESEARCH (2002)
Fractionation of isotopically labeled peptides in quantitative proteomics
RJ Zhang et al.
ANALYTICAL CHEMISTRY (2001)
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
DK Han et al.
NATURE BIOTECHNOLOGY (2001)
Significance analysis of microarrays applied to the ionizing radiation response
VG Tusher et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Share Paper
