Purpose | Data | Fit all methods | One line per method | One protein, all methods | Session info

Purpose | Simulated protein abundances | Visualization of not normalized data | Visualization of missing data | Computing standard deviations, mean and CV. | Normalize protein intensities and show diagnostic plots | Fit the model and compute contrasts | Gene Set Enrichment Analysis (GSEA) | Session Info | References

Documentation | Introduction | Installation | Quick start | Session info | References

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

Introduction | MSQC1 Peptide properties | Figure - reference L:H ratio versus the on-column amount | Data | Illustrations | Figure - Sigma mix peptide level signals | Figure - Volcano Plot | Figure - Ratio stability upon analyte dilution | Figure - Accuracy | Session information | References

Introduction | Problem: | Solution: Normalization | RT plot | 8 Technical Replicates RT plot | Dilution Series RT plot | LC Gradient Comparison | 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

Sample description | Data recording | Q Exactive HF-X | LC | MS | Fusion Lumos | mzXML conversion | Uploading to S3 | Usage | Session info | References

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

Introduction | Methods | Results | Conclusions

Recent changes and updates | Introduction | Data preparation | Analysis