From 5e2befa7d3cef04766f30290d9811b61373ce4fe Mon Sep 17 00:00:00 2001 From: chengxin Dai <37200167+daichengxin@users.noreply.github.com> Date: Wed, 9 Mar 2022 16:48:37 +0800 Subject: [PATCH 1/4] Add proteomics data acquisition method in openms.tsv --- sdrf_pipelines/openms/openms.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/sdrf_pipelines/openms/openms.py b/sdrf_pipelines/openms/openms.py index 7130d64..081b3dd 100644 --- a/sdrf_pipelines/openms/openms.py +++ b/sdrf_pipelines/openms/openms.py @@ -706,7 +706,8 @@ def writeOneTableExperimentalDesign(self, output_filename, legacy, sdrf, file2te def save_search_settings_to_file(self, output_filename, sdrf, f2c): f = open(output_filename, "w+") - open_ms_search_settings_header = ["URI", "Filename", "FixedModifications", "VariableModifications", "Label", + open_ms_search_settings_header = ["URI", "Filename", "FixedModifications", "VariableModifications", + "Proteomics data acquisition method", "Label", "PrecursorMassTolerance", "PrecursorMassToleranceUnit", "FragmentMassTolerance", "FragmentMassToleranceUnit", "DissociationMethod", "Enzyme"] @@ -722,6 +723,15 @@ def save_search_settings_to_file(self, output_filename, sdrf, f2c): for _0, row in sdrf.iterrows(): URI = row["comment[file uri]"] raw = row["comment[data file]"] + if "comment[proteomics data acquisition method]" not in row: + warning_message = "The comment[proteomics data acquisition method] column is missing, " \ + "default Data-Dependent Acquisition" + self.warnings[warning_message] = self.warnings.get(warning_message, 0) + 1 + acquisition_method = "Data-Dependent Acquisition" + else: + acquisition_method = row["comment[proteomics data acquisition method]"] + acquisition_method = acquisition_method.split(";")[0].split("=")[1] + if raw in raws: continue raws.append(raw) @@ -768,7 +778,8 @@ def save_search_settings_to_file(self, output_filename, sdrf, f2c): "sample', 'ITRAQ', and tmt labels in the format 'TMT131C'") f.write( - URI + "\t" + raw + "\t" + f2c.file2mods[raw][0] + "\t" + f2c.file2mods[raw][1] + "\t" + label + "\t" + + URI + "\t" + raw + "\t" + f2c.file2mods[raw][0] + "\t" + f2c.file2mods[raw][1] + "\t" + + acquisition_method + "\t" + label + "\t" + f2c.file2pctol[ raw] + "\t" + f2c.file2pctolunit[raw] + "\t" + f2c.file2fragtol[raw] + "\t" + f2c.file2fragtolunit[ raw] + "\t" + From ad8c8ca23eb1919391f52722fe725d703d90834a Mon Sep 17 00:00:00 2001 From: chengxin Dai <37200167+daichengxin@users.noreply.github.com> Date: Wed, 9 Mar 2022 16:49:07 +0800 Subject: [PATCH 2/4] Update setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8501a4a..8f98e65 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name="sdrf-pipelines", - version="0.0.20", + version="0.0.21", author="BigBio Team", author_email="ypriverol@gmail.com", description="Translate, convert SDRF to configuration pipelines", From 1bb2335d88cd019dc11f1337f674accb78e3470c Mon Sep 17 00:00:00 2001 From: chengxin Dai <37200167+daichengxin@users.noreply.github.com> Date: Wed, 9 Mar 2022 16:58:09 +0800 Subject: [PATCH 3/4] update test --- sdrf_pipelines/openms/openms.py | 2 +- .../testdata/PXD001819/expected_openms.tsv | 56 +++++++++---------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/sdrf_pipelines/openms/openms.py b/sdrf_pipelines/openms/openms.py index 081b3dd..fbc81bf 100644 --- a/sdrf_pipelines/openms/openms.py +++ b/sdrf_pipelines/openms/openms.py @@ -707,7 +707,7 @@ def writeOneTableExperimentalDesign(self, output_filename, legacy, sdrf, file2te def save_search_settings_to_file(self, output_filename, sdrf, f2c): f = open(output_filename, "w+") open_ms_search_settings_header = ["URI", "Filename", "FixedModifications", "VariableModifications", - "Proteomics data acquisition method", "Label", + "Proteomics Data Acquisition Method", "Label", "PrecursorMassTolerance", "PrecursorMassToleranceUnit", "FragmentMassTolerance", "FragmentMassToleranceUnit", "DissociationMethod", "Enzyme"] diff --git a/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv b/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv index b928239..2361b78 100644 --- a/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv +++ b/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv @@ -1,28 +1,28 @@ -URI Filename FixedModifications VariableModifications Label PrecursorMassTolerance PrecursorMassToleranceUnit FragmentMassTolerance FragmentMassToleranceUnit DissociationMethod Enzyme -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R1.raw UPS1_12500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R2.raw UPS1_12500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R3.raw UPS1_12500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R1.raw UPS1_125amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R2.raw UPS1_125amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R3.raw UPS1_125amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R1.raw UPS1_25000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R2.raw UPS1_25000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R3.raw UPS1_25000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R1.raw UPS1_2500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R2.raw UPS1_2500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R3.raw UPS1_2500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R1.raw UPS1_250amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R2.raw UPS1_250amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R3.raw UPS1_250amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R1.raw UPS1_50000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R2.raw UPS1_50000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R3.raw UPS1_50000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R1.raw UPS1_5000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R2.raw UPS1_5000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R3.raw UPS1_5000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw UPS1_500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R2.raw UPS1_500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R3.raw UPS1_500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R1.raw UPS1_50amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R2.raw UPS1_50amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R3.raw UPS1_50amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P +URI Filename FixedModifications VariableModifications Proteomics Data Acquisition Method Label PrecursorMassTolerance PrecursorMassToleranceUnit FragmentMassTolerance FragmentMassToleranceUnit DissociationMethod Enzyme +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R1.raw UPS1_12500amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R2.raw UPS1_12500amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R3.raw UPS1_12500amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R1.raw UPS1_125amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R2.raw UPS1_125amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R3.raw UPS1_125amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R1.raw UPS1_25000amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R2.raw UPS1_25000amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R3.raw UPS1_25000amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R1.raw UPS1_2500amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R2.raw UPS1_2500amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R3.raw UPS1_2500amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R1.raw UPS1_250amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R2.raw UPS1_250amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R3.raw UPS1_250amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R1.raw UPS1_50000amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R2.raw UPS1_50000amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R3.raw UPS1_50000amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R1.raw UPS1_5000amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R2.raw UPS1_5000amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R3.raw UPS1_5000amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw UPS1_500amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R2.raw UPS1_500amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R3.raw UPS1_500amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R1.raw UPS1_50amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R2.raw UPS1_50amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R3.raw UPS1_50amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P From 36b82190d24165507c0c8989f7cfcd789146cad4 Mon Sep 17 00:00:00 2001 From: chengxin Dai <37200167+daichengxin@users.noreply.github.com> Date: Wed, 9 Mar 2022 20:39:11 +0800 Subject: [PATCH 4/4] Update expected_openms.tsv --- .../testdata/PXD001819/expected_openms.tsv | 54 +++++++++---------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv b/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv index 2361b78..dcc74cb 100644 --- a/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv +++ b/sdrf_pipelines/testdata/PXD001819/expected_openms.tsv @@ -1,28 +1,28 @@ URI Filename FixedModifications VariableModifications Proteomics Data Acquisition Method Label PrecursorMassTolerance PrecursorMassToleranceUnit FragmentMassTolerance FragmentMassToleranceUnit DissociationMethod Enzyme -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R1.raw UPS1_12500amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R2.raw UPS1_12500amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R3.raw UPS1_12500amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R1.raw UPS1_125amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R2.raw UPS1_125amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R3.raw UPS1_125amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R1.raw UPS1_25000amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R2.raw UPS1_25000amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R3.raw UPS1_25000amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R1.raw UPS1_2500amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R2.raw UPS1_2500amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R3.raw UPS1_2500amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R1.raw UPS1_250amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R2.raw UPS1_250amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R3.raw UPS1_250amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R1.raw UPS1_50000amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R2.raw UPS1_50000amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R3.raw UPS1_50000amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R1.raw UPS1_5000amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R2.raw UPS1_5000amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R3.raw UPS1_5000amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw UPS1_500amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R2.raw UPS1_500amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R3.raw UPS1_500amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R1.raw UPS1_50amol_R1.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R2.raw UPS1_50amol_R2.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P -ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R3.raw UPS1_50amol_R3.raw Carbamidomethyl (C) "Acetyl (Protein N-term),Oxidation (M)" Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R1.raw UPS1_12500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R2.raw UPS1_12500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R3.raw UPS1_12500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R1.raw UPS1_125amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R2.raw UPS1_125amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R3.raw UPS1_125amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R1.raw UPS1_25000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R2.raw UPS1_25000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R3.raw UPS1_25000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R1.raw UPS1_2500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R2.raw UPS1_2500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R3.raw UPS1_2500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R1.raw UPS1_250amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R2.raw UPS1_250amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R3.raw UPS1_250amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R1.raw UPS1_50000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R2.raw UPS1_50000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R3.raw UPS1_50000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R1.raw UPS1_5000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R2.raw UPS1_5000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R3.raw UPS1_5000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw UPS1_500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R2.raw UPS1_500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R3.raw UPS1_500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R1.raw UPS1_50amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R2.raw UPS1_50amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P +ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R3.raw UPS1_50amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P