Introduction | Implementation | Example data | Results | Use Case I - Analyzing Orbitrap Spectra | Use Case II - iRT Regression for System Suitability Monitoring | Extension | Benchmark | mZ and intensity vectors have different lengths. What shall I do? | Howto write the rawrr::readFileHeader() output into json file? | System and session information | .NET information | References

Usage | R command line | Input | readRaw - read Orbitrap raw file | Output - Visualization | Launching the shiny application | FAQ | I would like to load multiple files into a single data.frame to do comparisons; what is the preferred method for doing so? | References | Session information

Requirements | Load data | Usage | Application example | Peptide Identification | Class extension | Export Mascot Generic Format File | Procesing queue | Evaluation | Efficiency - I/O Benchmark | Effectiveness | Session information | References

Introduction | The Usage | Input - using the U.S. state Facts and Figures Dataset | Compute Pseudo Dual Graph (PD) | Apply a Metaheuristic | Objective Functions | Output | Application | Rectangular Map Approximation | state.x77[, 'Population'] | state.x77[, 'Income'] | state.x77[, 'Frost'] | Synthetic input maps - checkerboard | History | Session Info | References

Introduction | Workflow | Prologue - How to get the input for the specL package? | Read from redundant plus non-redundant blib files | Read from Mascot result files | Annotate protein IDs using FASTA | Generate the spectral library (assay) | Normalizing the retention time using iRT peptides | Generate the spectral library having no iRTs | Write output to file | Epilogue | What can I do with that library now? | Benchmark | Acknowledgement | TODO for next releases | Session information | References

Requirements | Input | Parameter | Define the fragment ions of interest | Read the sqlite files | Protein (re)-annotation | Peptides used for RT normalization | Generate the ion library | Library Generation Summary | Output | Remarks | Session info | References

Illustrations

Related Work | Get Data In – Preprocessing | Peptide Identification | Quantification | Pressure Profiles QC | Session information

Howto get the software and data | Finding the Marker Ions | Demonstartion | Session information

Recent changes and updates | Introduction | Data preparation | Analysis