fix typos in version 2 for f1000

CambridgeCentreForProteomics · Sep 13, 2024 · b0a7d30 · b0a7d30
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diff --git a/workflow_expressions.Rmd b/workflow_expressions.Rmd
@@ -3660,3 +3660,50 @@ against implementing such filtering at this stage since decisions regarding
 thresholds will likely be influenced by the quality of data output, as
 demonstrated later in this workflow. Instead, thresholds for the three
 aforementioned parameters were set to 0 during the identification search.
+
+
+## Using this workflow with MaxQuant data
+
+This workflow was written for proteomics data processed using the Proteome
+Discoverer software. Nevertheless, the workflow and basic principles discussed
+are also applicable to the output of any similar proteomics raw data processing
+software, including MaxQuant. Below we outline the differences to be aware of 
+when following this workflow using MaxQuant output text files. The code as 
+written will require some minor modifications to work properly with MaxQuant 
+formatted data.
+
+1. The rough equivalent of the PSMs.txt file output by Proteome Discoverer is 
+the evidence.txt file output by MaxQuant.
+
+2. Decoy PSMs (known false discoveries which are used to calculate false discovery
+rate) are automatically filtered out by Proteome Discoverer, but this is not the 
+case with MaxQuant. Hence when working with MaxQuant outputs it is important to
+filter out rows with '+' in the `Reverse` column.
+
+3. Equivalent column names and the type of data contained are described here. 
+Ellipses are put where there no equivalent column exists.
+
+In PD the file `PSMs.txt` is equivalent to the MaxQuant `evidence.txt` file. 
+Equivalent column names are shown in the table below:
+
+* `Abundance` (float) = `Reporter.intensity.corrected` (integer)
+* `Sequence` (string) = `Sequence` (string)
+* `Master.Protein.Accessions` (string) = `Leading.proteins` (string)
+* `Master.Protein.Descriptions` (string) = ...
+* `Contaminants` (string, True or False) = `Potential.contaminant` (string, + or blank)
+* ... = `Reverse` (string, + or blank)
+* `Rank` (integer) = ...
+* `Search.Engine.Rank` (integer) = ...
+* `PSM.Ambiguity` (string) = ...
+* `Number.of.Protein.Groups` (integer) = ... (you might calculate this by counting the number of ; in the Leading.proteins column and adding 1)
+* `Average.Reporter.SN` (float) = ... (you might calculate the average reporter ion intensity and threshold based on that instead)
+* `Isolation.Interference.in.Percent` (float) = `PIF` (float, to get the data in exactly the same format you have to calculate (1 - PIF)*100)
+* `SPS.Mass.Matches.in.Percent` (integer) = ...
+
+(PD Proteins.txt column = MaxQuant proteinGroups.txt column):
+
+* `Accession` (string) = `Majority.protein.IDs` (string)
+* `Protein.FDR.Confidence.Combined` (string; High, Medium, or Low) = `Q.value` (float, a Proteome Discoverer protein FDR of 'High' is equivalent to a Q.value < 0.01)
+
+
+# References
diff --git a/workflow_expressions.log b/workflow_expressions.log
diff --git a/workflow_expressions.pdf b/workflow_expressions.pdf
diff --git a/workflow_expressions.tex b/workflow_expressions.tex
diff --git a/workflow_expressions_files/figure-latex/GO_enrichment_plot-1.pdf b/workflow_expressions_files/figure-latex/GO_enrichment_plot-1.pdf
diff --git a/workflow_expressions_files/figure-latex/MA_plot-1.pdf b/workflow_expressions_files/figure-latex/MA_plot-1.pdf
diff --git a/workflow_expressions_files/figure-latex/correlation_plot_2-1.pdf b/workflow_expressions_files/figure-latex/correlation_plot_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/correlation_plot_3-1.pdf b/workflow_expressions_files/figure-latex/correlation_plot_3-1.pdf
diff --git a/workflow_expressions_files/figure-latex/lfq_RT-1.pdf b/workflow_expressions_files/figure-latex/lfq_RT-1.pdf
diff --git a/workflow_expressions_files/figure-latex/lfq_imputation_4-1.pdf b/workflow_expressions_files/figure-latex/lfq_imputation_4-1.pdf
diff --git a/workflow_expressions_files/figure-latex/lfq_mass_accuracy-1.pdf b/workflow_expressions_files/figure-latex/lfq_mass_accuracy-1.pdf
diff --git a/workflow_expressions_files/figure-latex/lfq_missing_data_2-1.pdf b/workflow_expressions_files/figure-latex/lfq_missing_data_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/plotSA-1.pdf b/workflow_expressions_files/figure-latex/plotSA-1.pdf
diff --git a/workflow_expressions_files/figure-latex/protein_pca_plot-1.pdf b/workflow_expressions_files/figure-latex/protein_pca_plot-1.pdf
diff --git a/workflow_expressions_files/figure-latex/pvalue_histogram-1.pdf b/workflow_expressions_files/figure-latex/pvalue_histogram-1.pdf
diff --git a/workflow_expressions_files/figure-latex/qfeatures_links_plots-1.pdf b/workflow_expressions_files/figure-latex/qfeatures_links_plots-1.pdf
diff --git a/workflow_expressions_files/figure-latex/support_plots-1.pdf b/workflow_expressions_files/figure-latex/support_plots-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_RT-1.pdf b/workflow_expressions_files/figure-latex/tmt_RT-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_coisolation_2-1.pdf b/workflow_expressions_files/figure-latex/tmt_coisolation_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_ion_injection_1-1.pdf b/workflow_expressions_files/figure-latex/tmt_ion_injection_1-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_ion_injection_2-1.pdf b/workflow_expressions_files/figure-latex/tmt_ion_injection_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_mass_accuracy-1.pdf b/workflow_expressions_files/figure-latex/tmt_mass_accuracy-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_missing_data_2-1.pdf b/workflow_expressions_files/figure-latex/tmt_missing_data_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_normalisation_2-1.pdf b/workflow_expressions_files/figure-latex/tmt_normalisation_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_sn_ratio_2-1.pdf b/workflow_expressions_files/figure-latex/tmt_sn_ratio_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_sps_matches_2-1.pdf b/workflow_expressions_files/figure-latex/tmt_sps_matches_2-1.pdf
diff --git a/workflow_expressions_files/figure-latex/tmt_transformations-1.pdf b/workflow_expressions_files/figure-latex/tmt_transformations-1.pdf
diff --git a/workflow_expressions_files/figure-latex/volcano_plot-1.pdf b/workflow_expressions_files/figure-latex/volcano_plot-1.pdf