Peptide Identification by Tandem Mass Spectrometry with Alternate Fragmentation Modes

Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

(2012) Katalin F. Medzihradszky et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

Venoms as a platform for human drugs: translating toxins into therapeutics

(2011) Glenn F King   EXPERT OPINION ON BIOLOGICAL THERAPY

Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment

(2011) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Universal and Confident Phosphorylation Site Localization Using phosphoRS

(2011) Thomas Taus et al.   JOURNAL OF PROTEOME RESEARCH

Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods

(2011) Yufeng Shen et al.   JOURNAL OF PROTEOME RESEARCH

Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

(2011) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

Development of a combined chemical and enzymatic approach for the mass spectrometric identification and quantification of aberrant N-glycosylation

(2011) Rui Chen et al.   Journal of Proteomics

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Tandem mass spectrometry strategies for phosphoproteome analysis

(2011) Amanda M. Palumbo et al.   MASS SPECTROMETRY REVIEWS

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics

(2011) Mark P. Jedrychowski et al.   MOLECULAR & CELLULAR PROTEOMICS

A Face in the Crowd: Recognizing Peptides Through Database Search

(2011) Jimmy K. Eng et al.   MOLECULAR & CELLULAR PROTEOMICS

Anticonvulsant neuropeptides as drug leads for neurological diseases

(2011) Charles R. Robertson et al.   NATURAL PRODUCT REPORTS

Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells

(2011) Åsa Jufvas et al.   PLoS One

Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides

(2011) Min-Sik Kim et al.   PROTEOMICS

An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays

(2010) Hong Fang et al.   BMC BIOINFORMATICS

The significance, development and progress of high-throughput combinatorial histone code analysis

(2010) Nicolas L. Young et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Post-translational modifications of protein biopharmaceuticals

(2010) Gary Walsh   DRUG DISCOVERY TODAY

Gas-Phase Rearrangements Do Not Affect Site Localization Reliability in Phosphoproteomics Data Sets

(2010) Mike Aguiar et al.   JOURNAL OF PROTEOME RESEARCH

Evaluation of Metalloendopeptidase Lys-N Protease Performance under Different Sample Handling Conditions

(2010) Nadia Taouatas 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

pNovo:De novoPeptide Sequencing and Identification Using HCD Spectra

(2010) Hao Chi et al.   JOURNAL OF PROTEOME RESEARCH

Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

(2010) Nagarjuna Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Improving Software Performance for Peptide Electron Transfer Dissociation Data Analysis by Implementation of Charge State- and Sequence-Dependent Scoring

(2010) Peter R. Baker et al.   MOLECULAR & CELLULAR PROTEOMICS

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Confident Phosphorylation Site Localization Using the Mascot Delta Score

(2010) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

The pros and cons of peptide-centric proteomics

(2010) Mark W Duncan et al.   NATURE BIOTECHNOLOGY

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

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

(2010) Tommy Nilsson et al.   NATURE METHODS

RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics

(2010) Gelio Alves et al.   PLoS One

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

(2010) Eric W. Deutsch et al.   PROTEOMICS

Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

(2009) Saiful M. Chowdhury et al.   ANALYTICAL CHEMISTRY

De novopeptide sequencing by tandem MS using complementary CID and electron transfer dissociation

(2009) Andreas Bertsch et al.   ELECTROPHORESIS

Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing

(2009) Ritendra Datta et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets

(2009) Marina Spivak et al.   JOURNAL OF PROTEOME RESEARCH

Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy

(2009) F. R. Depontieu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry

(2009) D. L. Swaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides

(2009) R. J. Chalkley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plk1 Self-Organization and Priming Phosphorylation of HsCYK-4 at the Spindle Midzone Regulate the Onset of Division in Human Cells

(2009) Mark E. Burkard et al.   PLOS BIOLOGY

Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation

(2008) Henrik Molina et al.   ANALYTICAL CHEMISTRY

Evaluation of the Low-Specificity Protease Elastase for Large-Scale Phosphoproteome Analysis

(2008) Bin Wang et al.   ANALYTICAL CHEMISTRY

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry

(2008) N. Bandeira et al.   BIOINFORMATICS

Enhancing Peptide Identification Confidence by Combining Search Methods

(2008) Gelio Alves et al.   JOURNAL OF PROTEOME RESEARCH

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

(2008) Brian C. Searle et al.   JOURNAL OF PROTEOME RESEARCH

Electron Capture/Transfer versus Collisionally Activated/Induced Dissociations: Solo or Duet?

(2008) Roman A. Zubarev et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Spectral Dictionaries

(2008) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Decision tree–driven tandem mass spectrometry for shotgun proteomics

(2008) Danielle L Swaney et al.   NATURE METHODS