making separate repo for mouse lens with MQ

Author: pwilmart

MQ_analysis.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX

MQ_data_prep_steps.txt

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+proteinGroups.txt prep for mouse lens data
+
+x Open Excel with blank sheet
+x Use menues or other mechanism in Excel to open proteinGroups.txt file
+x 	We want the Text Import Wizard to activate
+x 	Click "next" on first two steps (delimited and tab as separator)
+x 	In third step, make sure any columns with gene names are text format (7th column)
+x After import, save file as XLSX format (and name something more distinct)
+x Add a spacer column at the far right of the sheet (Col. FN) and fill with "blank"
+x Add a "flag" column (FO) to denote rejected proteins (decoys, contams, missing data)
+x Populate the "flag" column with "z" (later we will sort descending)
+x Add 4 extra rows at top of sheet (so headers are in Row 5)
+x Make header row "bold"
+x Allow header cells to wrap text (cell formatting)
+x Save sheet (save often)
+
+x Select Row 5 and turn on column filters
+x Show "+" for Col FC ("Reverse") to show decoys
+x Replace "z" in Flag column (FO) with "decoy" and fill down
+x Reset column filter on FC
+x Show "+" for Col FD ("Potential contaminant") to show contaminants
+x Replace "z" in Flag column (FO) with "contam" and fill down
+x Reset column filter on FD
+x Show any rows with "keratin" in "Protein names" (Col F)
+x Flag any additional keratins as "contams" in Flag column
+x Look for "albumin" and also flag as contam
+x Clear filter on Col. F
+
+x Add a "Counter" column (FP)
+x 	fill column with the number "1"
+x 	make sure the values stop at the end of the table (row 6364)
+x 	enter formula: "=SUBTOTAL(109,FP6:FP6501)" in cell FP4
+
+x Sort descending on Flag column (FO)
+x Insert blank row at bottom of table between contams and decoys and other proteins
+
+["mouse_lens_3TMTs_proteinGroups_int1.xlsx" is save at this point]
+
+x Select Row 5 and turn off column filters
+x Locate the reporter ion columns of interest (CL:DO) and add sample key in Row 4 above
+x 	Do not use any "corrected" reporter ion columns
+x 	There are experiment-wide columns (Cols AD-AW)
+x 	There are columns for each experimental sample (cols BH-DO)
+x 	We want columns CL through DO
+x 	Add sample key above reporter channels (they are in increasing mass order)
+x 		The first 6 channels were used for the time point (in increasing order)
+x 		Note that N forms are lighter than C forms
+x 			An alphabetical ordering is not the same as a mass-based ordering
+
+x We need to get columns for the same condition together for counting of missing data
+x We will need 4 columns for counters (one for each TMT experiment and a combined col.)
+x Copy the Exp. 1 data (CL:CQ) to columns FU:FZ
+x Copy the Exp. 2 data (CV:DA) to columns GA:GF
+x Copy the Exp. 3 data (DF:DK) to columns GG:GL
+x Replace the column names (row 5) with sample names
+x Label column FQ as "keeper"
+x Label column FR "missing_1"
+x Label column FS "missing_2"
+x Label column FT "missing_3"
+x Fill FQ with this formula: "=COUNTIF(FR6:FT6,"=ok")"
+x Fill FR with this formula: "=IF(COUNTIF(FU6:FZ6, ">1")>=5, "ok", "missing")"
+x Fill FS with this formula: "=IF(COUNTIF(GA6:GF6, ">1")>=5, "ok", "missing")"
+x Fill FT with this formula: "=IF(COUNTIF(GG6:GL6, ">1")>=5, "ok", "missing")"
+x 	In these discovery experiments, we want to cast a wide net
+x 	We want to allow a maximum of one missed reporter ion in each experiment
+
+["mouse_lens_3TMTs_proteinGroups_int2.xlsx" is save at this point]
+
+x Select Row 5 and turn column filters back on
+x Sort column FQ descending (we will keep rows with a value of "3")
+x Insert a blank row when count goes from "3" to "2" (rows 3873 and 3874)
+x Replace "z" in Flag column (FO) with "missing data" for rows 3875:6222
+ 
+x Copy cells B5:B3873 (Majority protein IDs) to cells GM5:GM3873
+x Rename column header to "Accession" (cell GM5)
+x [Optional:
+x 	Convert text-to-columns as delimited with semicolon checked
+x 	Select a bunch of columns (eg. GN to HT) and clear contents]
+x Add a new tab
+x Rename tab to "MQ_prepped_data"
+x Copy cells FU5:GM3873 to new tab (paste in at cell A1)
+x Save workbook [a "mouse_lens_3TMTs_protenGroups_int3.xlsx" file was created here]
+x Go to "MQ_prepped_data" tab
+x Save As "MQ_prepped_data.csv" in CSV format (save just the selected tab)
+x Excel may give you several warnings
+x Quit Excel
+
+Zero replacements and data normalizations will be done in R
+	
+