pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Peptide Identification by Database Search of Mixture Tandem Mass Spectra

(2011) Jian Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies

(2010) Stephane Houel et al.   JOURNAL OF PROTEOME RESEARCH

Peptide Identification from Mixture Tandem Mass Spectra

(2010) Jian Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

YADA: a tool for taking the most out of high-resolution spectra

(2009) Paulo C. Carvalho et al.   BIOINFORMATICS

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

(2009) Navdeep Jaitly et al.   BMC BIOINFORMATICS

Review of Peak Detection Algorithms in Liquid-Chromatography-Mass Spectrometry

(2009) Jianqiu Zhang et al.   CURRENT GENOMICS

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics

(2009) Peter Mortensen et al.   JOURNAL OF PROTEOME RESEARCH

Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity

(2009) Jamie Sherman et al.   MOLECULAR & CELLULAR PROTEOMICS

Isotopic Peak Intensity Ratio Based Algorithm for Determination of Isotopic Clusters and Monoisotopic Masses of Polypeptides from High-Resolution Mass Spectrometric Data

(2008) Kunsoo Park et al.   ANALYTICAL CHEMISTRY

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

(2008) A. M. Mayampurath et al.   BIOINFORMATICS

Detection of co-eluted peptides using database search methods

(2008) Gelio Alves et al.   Biology Direct

Precursor-Ion Mass Re-Estimation Improves Peptide Identification on Hybrid Instruments

(2008) Roland Luethy et al.   JOURNAL OF PROTEOME RESEARCH

DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

(2008) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses

(2008) Alexander Scherl et al.   PROTEOMICS