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Journal Article
Journal of Proteomics, ISSN 1874-3919, 05/2014, Volume 103, Issue 100, pp. 1 - 14
Journal Article
Data in Brief, ISSN 2352-3409, 06/2018, Volume 18, pp. 1 - 8
Over the last years, the SWATH data-independent acquisition protocol (Sequential Window acquisition of All THeoretical mass spectra) has become a cornerstone... 
Neural stem cells | Neuroscience | SWATH | Proteomics
Journal Article
Acta Veterinaria Scandinavica, ISSN 1477-5956, 11/2013, Volume 11, Issue Suppl 1, pp. S10 - S10
Background: The sequence database searching has been the dominant method for peptide identification, in which a large number of peptide spectra generated from... 
SHOTGUN PROTEOMICS | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | VALIDATION | MODEL | MS/MS | DATA SETS | MASS-SPECTROMETRY | PROTEIN IDENTIFICATION | DATABASE SEARCH | Proteins | Studies | Enzymes | Algorithms | Yeast | Peptides | Classification | Science | Experiments | Data bases
Journal Article
2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 10/2012, pp. 602 - 609
Peptide identification is a critical step to understand the proteome in cells and tissue. Typically, high-throughput peptide spectra generated in the MS/MS... 
Support vector machines | Proteins | Peptides | fuzzy support vector machine (SVM) | fuzzy clustering | Linear programming | Educational institutions | peptide identification | peptide spectrum matches (PSMs) | Indexes | Peptide spectrum matches (PSMs) | Peptide identification | Fuzzy clustering | Fuzzy support vector machine (SVM)
Conference Proceeding
07/2010, ISBN 0470681993, 13
Mass spectrometry based proteomic methods generate a large quantity of complex highly dimensional data, particularly when used to analyse intact biological... 
peptide spectrum match (PSM)‐collection of statistics | data mining for predictive proteomics | Artificial Neural Networks (ANNs)‐algorithms determining solution to problems iteratively fitting a complex function (model) to data | noise reduction, baseline removal and normalization | vectors explaining variation in data‐using principal component analysis | biological sample analysis using mass spectrometry (MS) based methods‐number of challenges | proteomics data mining workflow | feature selection method‐Support Vector Machines Recursive Feature Elimination (SVMRFE) | pre‐processing MS data | statistical analysis of 2D gels and mass spectral data analysis | Feature selection method-Support Vector Machines Recursive Feature Elimination (SVMRFE) | Proteomics data mining workflow | Artificial Neural Networks (ANNs)-algorithms determining solution to problems iteratively fitting a complex function (model) to data | Noise reduction, baseline removal and normalization | Statistical analysis of 2D gels and mass spectral data analysis | Peptide spectrum match (PSM)-collection of statistics | Vectors explaining variation in data-using principal component analysis | Biological sample analysis using mass spectrometry (MS) based methods-number of challenges | Pre-processing MS data | Data mining for predictive proteomics
Book Chapter
Journal of Proteome Research, ISSN 1535-3893, 09/2013, Volume 12, Issue 9, pp. 4240 - 4247
Journal Article
Current Protocols in Bioinformatics, ISSN 1934-3396, 2012, Volume Chapter 13, Issue 40, p. Unit13.19
PatternLab for proteomics is a self-contained computational environment for analyzing shotgun proteomic data. Recent improvements incorporate modules to... 
Protein identification | filtering PSMs | Semi-labeled decoy approach | Quantitative proteomics | Dniaf | Software | Proteins - chemistry | Proteomics - methods | Mass Spectrometry - methods | Databases, Protein
Journal Article
Journal of Proteomics, ISSN 1874-3919, 02/2014, Volume 98, pp. 150 - 158
Shotgun proteomics is a powerful technology to study the protein population of a biological system. This approach employs tandem mass spectrometry for amino... 
SEQUEST | Shotgun proteomics | PSM | Pearson's χ2 statistic | Pearson's χ | statistic | SPECTROMETRY DATA | Pearson's chi statistic | DATABASE | PEPTIDE IDENTIFICATION | BIOCHEMICAL RESEARCH METHODS | PROTEIN IDENTIFICATION | PREDICTION | PROTEOMICS | TOOL | Mass spectrometry | Usage
Journal Article
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