Quantification of oxidative modification of human serum albumin by MRM-HR
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: Ikuo Kashiwakura
PROVIDER: PXD025947 | JPOST Repository | Thu May 12 00:00:00 BST 2022
REPOSITORIES: jPOST
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 191120_major_10_MRM-HR.wiff | Wiff | |||
| 191120_major_23_MRM-HR.wiff | Wiff | |||
| 191120_major_25_MRM-HR.wiff | Wiff | |||
| 191120_major_26_MRM-HR.wiff | Wiff | |||
| 191120_major_27_MRM-HR.wiff | Wiff |
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Publications
Detection of biological responses to low-dose radiation in humans.
Yamaguchi Masaru M Tatara Yota Y Nugraha Eka Djatnika ED Ramadhani Dwi D Tamakuma Yuki Y Sato Yoshiaki Y Miura Tomisato T Hosoda Masahiro M Yoshinaga Shinji S Syaifudin Mukh M Kashiwakura Ikuo I Tokonami Shinji S
Free radical biology & medicine 20220418
It has been considered difficult to detect the biological effects of low-dose radiation exposure below approximately 100 mSv in humans. Serum proteomic analysis and oxidative modification profiling were conducted with blood samples collected from residents of a newly discovered high-level natural background radiation area (annual effective dose approximately 50 mSv y<sup>-1</sup>) and normal-level area (1.22 mSv y<sup>-1</sup>) in Mamuju, Indonesia, where many people have been living for generat ...[more]
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Project description:Two sampling areas were focused in this study; Tande tande hamlet as high-level natural background radiation area (HBRA) and Topoyo sub-district as normal level background radiation area (NBRA), which was done under coordination with Local Health Office. The former located in 2° 44’ 38.3’’ south latitude/ 118° 48’ 47’’ east longitude belongs to Northern Botteng village in Simboro district of Mamuju city, and the population of the hamlet is 350 people in 2017 on an area of 16.22 km2 according to the information of BPS-Statistics of Mamuju Regency 2018. The latter located in 1° 59’ 38.3’’ south latitude/ 119° 28’ 16.7’’ east longitude belongs to Topoyo sub-district of Mamuju Tengah city about 120 km from Mamuju city, and the population of the sub-district is 31,888 people with 16,463 men (51.63%) and 15,425 women (48.37%) in 2017 on an area of 844.80 km2 according to the information of BPS-Statistics of Mamuju Regency 2019. 26 healthy adult inhabitants (13 males and 13 females) from Tande tande hamlet and 23 healthy adult inhabitants (14 males and 9 females) from Topoyo sub-district were included in this study. All volunteers were informed about the nature, aims, and intention of the study and signed a consent form and questionnaire to obtain information on age and occupation and another biodata before providing blood samples. Any individuals suffering from an illness or taking medication were excluded. Peripheral blood samples then were obtained from the antecubital vein using BD Vacutainer tubes in the morning and placed at room temperature for at least 30 min to allow blood-clotting. Sera was collected by centrifugation at 1,200 ×g for 10 min at 4°C and stored at - 80°C until the analysis.
2 μl of sera was diluted with 198 μl of 50 mM ammonium bicarbonate. The serum proteins were precipitated by adding 1 ml of acetone. The precipitated proteins were collected by centrifugation at 15,000 ×g for 10 min. The precipitate was resuspended in 10 μl of 500 mM ammonium bicarbonate and denatured with an equivalent volume of trifluoroethanol and 5 μl of 200 mM DTT. The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 10 μl of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 5 μl of 200 mM DTT. The samples were then mixed with 320 μl of 100 mM ammonium bicarbonate. The samples were incubated with 5 μg trypsin (TPCK treated, AB Sciex) at 37°C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography on a trap and elution configuration using a nano trap column (350 μm × 0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm × 15 cm, 3 μm, 120 Å, AB Sciex) at 300 nl/min with a 90 min linear gradient of 8% to 30% acetonitrile in 0.1% formic acid, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% formic acid. The mass spectrometer operated in information-dependent acquisition mode, scanning full spectra (400-1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100-1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. Rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated by Analyst TF 1.7.1 software (AB Sciex). For data-independent acquisition (SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at 50 ms accumulation time for m/z 400-1250. MS/MS SWATH scans were set at 5 Da window overlapping by 1 Da for m/z 400-1250 and varied on each side of the mass range. The total cycle time was 9.6 s. Rolling collision energy parameter script was used for automatically controlling the collision energy.
2022-05-12 | PXD025946 | JPOST Repository
Project description:10 µm formalin-fixed paraffin-embedded tissue sections were deparaffinized with xylene; homogenization was performed in lysis-buffer (20 mM Tris-HCl, pH 8.8, 200 mM glycine, 200 mM DTT, 4% SDS)in an ultrasonic bath; samples were incubated under continuous agitation first at 99 °C for 30 min, then at 80 °C for 60 min, afterwards centrifuged at 12,000xg for 10 min. 50 µg of protein lysate were further processed according the GASP (Gel-assisted sample preparation) protocol; peptide identification (IDA, information dependent acquisition) and SWATH measurements by LC-MS/MS on TripleTOF5600 (AB Sciex)
2020-05-18 | PXD012317 | Pride
Project description:After a week of acclimatization, 8-week-old mice were randomly divided into 4 groups consisting of more than 8 mice per group, and subjected to varying total body irradiation (TBI) doses of 0, 0.5, 1 or 3 Gy of X-rays (150 kVp, 20 mA, 0.5-mm aluminum and 0.3-mm copper filters) at a dose rate of 1.0 Gy/min using an MBR-1520R X-ray generator (Hitachi Medical, Tokyo, Japan). Peripheral blood was harvested 24 h after TBI from orbital venous plexus of mice anesthetized using isoflurane (Powerful Isoful; Zoetis, London, UK) by capillary tube, and placed at room temperature for at least 30 min to allow blood-clotting. Sera was collected by centrifugation at 1,200 ×g for 10 min and stored at - 80°C until the analysis. In addition, Sera collected from non-irradiated mice was subjected to varying TBI doses of 0, 0.5, 1 or 3 Gy of X-rays and incubated at 37°C for 24 h and stored at - 80°C until the analysis.
2 μl of sera was diluted with 198 μl of 50 mM ammonium bicarbonate. The serum proteins were precipitated by adding 1 ml of acetone. The precipitated proteins were collected by centrifugation at 15,000 ×g for 10 min. The precipitate was resuspended in 10 μl of 500 mM ammonium bicarbonate and denatured with an equivalent volume of trifluoroethanol and 5 μl of 200 mM DTT. The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 10 μl of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 5 μl of 200 mM DTT. The samples were then mixed with 320 μl of 100 mM ammonium bicarbonate. The samples were incubated with 5 μg trypsin (TPCK treated, AB Sciex) at 37°C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography on a trap and elution configuration using a nano trap column (350 μm × 0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm × 15 cm, 3 μm, 120 Å, AB Sciex) at 300 nl/min with a 90 min linear gradient of 8% to 30% acetonitrile in 0.1% formic acid, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% formic acid. The mass spectrometer operated in information-dependent acquisition mode, scanning full spectra (400-1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100-1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. Rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated by Analyst TF 1.7.1 software (AB Sciex).
2022-05-12 | PXD025948 | JPOST Repository
Project description:Formalin fixed paraffin-embedded pancreas tissues were deparaffinized by two changes of xylene and washed with descending concentrations of ethanol. Proteins in the deparaffinized tissues were extracted in 20%(w/v) of 200 mM Tris-HCl (pH 8.8) containing 2% SDS and 0.2 M DTT followed by incubation at 100˚C for 20 min and 80˚C for 2 h with shaking. The extracted proteins were precipitated by adding acetone. The precipitated proteins were resuspended in 10 μl of 500 mM ammonium bicarbonate and denatured with an equivalent volume of trifluoroethanol. Free cysteine residues were alkylated with 4 μl of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 1 μl of 200 mM DTT. The samples were then mixed with 300 μl of 100 mM ammonium bicarbonate. Fifteen microliters of the samples was diluted with 85 μl of 100 mM ammonium bicarbonate and incubated with 1 μg of trypsin at 37˚C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography on a trap and elution configuration using a nano trap column (350 μm × 0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm × 15 cm, 3 μm, 120 Å, AB Sciex) at 300 nl/min with a 90 min linear gradient of 8% to 30% acetonitrile in 0.1% formic acid, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% formic acid. The mass spectrometer operated in information-dependent acquisition mode, scanning full spectra (400-1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100-1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. Rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated by Analyst TF 1.7.1 software (AB Sciex). For data-independent acquisition (SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at 50 ms accumulation time for m/z 400-1250. MS/MS SWATH scans were set at 5 Da window overlapping by 1 Da for m/z 400-1250 and varied on each side of the mass range. The total cycle time was 9.6 s. Rolling collision energy parameter script was used for automatically controlling the collision energy.
2021-10-27 | PXD025975 | JPOST Repository
Project description:After a week of acclimatization, 8-week-old mice were randomly divided into 4 groups consisting of more than 8 mice per group, and subjected to varying total body irradiation (TBI) doses of 0, 0.5, 1 or 3 Gy of X-rays (150 kVp, 20 mA, 0.5-mm aluminum and 0.3-mm copper filters) at a dose rate of 1.0 Gy/min using an MBR-1520R X-ray generator (Hitachi Medical, Tokyo, Japan). Peripheral blood was harvested 24 h after TBI from orbital venous plexus of mice anesthetized using isoflurane (Powerful Isoful; Zoetis, London, UK) by capillary tube, and placed at room temperature for at least 30 min to allow blood-clotting. Sera was collected by centrifugation at 1,200 ×g for 10 min and stored at - 80°C until the analysis. In addition, Sera collected from non-irradiated mice was subjected to varying TBI doses of 0, 0.5, 1 or 3 Gy of X-rays and incubated at 37°C for 24 h and stored at - 80°C until the analysis.
2 μl of sera was diluted with 198 μl of 50 mM ammonium bicarbonate. The serum proteins were precipitated by adding 1 ml of acetone. The precipitated proteins were collected by centrifugation at 15,000 ×g for 10 min. The precipitate was resuspended in 10 μl of 500 mM ammonium bicarbonate and denatured with an equivalent volume of trifluoroethanol and 5 μl of 200 mM DTT. The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 10 μl of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 5 μl of 200 mM DTT. The samples were then mixed with 320 μl of 100 mM ammonium bicarbonate. The samples were incubated with 5 μg trypsin (TPCK treated, AB Sciex) at 37°C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography on a trap and elution configuration using a nano trap column (350 μm × 0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm × 15 cm, 3 μm, 120 Å, AB Sciex) at 300 nl/min with a 90 min linear gradient of 8% to 30% acetonitrile in 0.1% formic acid, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% formic acid. The mass spectrometer operated in information-dependent acquisition mode, scanning full spectra (400-1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100-1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. Rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated by Analyst TF 1.7.1 software (AB Sciex). For data-independent acquisition (SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at 50 ms accumulation time for m/z 400-1250. MS/MS SWATH scans were set at 5 Da window overlapping by 1 Da for m/z 400-1250 and varied on each side of the mass range. The total cycle time was 9.6 s. Rolling collision energy parameter script was used for automatically controlling the collision energy.
2022-05-12 | PXD025950 | JPOST Repository
Project description:The precipitated proteins from whole cells were resuspended in 50 μl of 500 mM ammonium bicarbonate containing 8 M urea, and reduced with 5 μl of 200 mM DTT. The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 10 μl of 200 mM iodoacetamide for 60 min at room temperature in the dark, and the remaining iodoacetamide was quenched by adding 5 μl of 200 mM DTT. The samples were then mixed with 320 μl of 100 mM ammonium bicarbonate. The samples were incubated with 5 μg trypsin (AB Sciex) at 37°C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid and analyzed with liquid chromatography (LC)-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using LC on a trap and elution configuration using a nano trap column (350 μm × 0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm × 15 cm, 3 μm, 120 Å, AB Sciex) at 300 nl/min with a 90-min linear gradient of 8% to 30% acetonitrile in 0.1% formic acid, and then, with a 10-min linear gradient of 30% to 40% acetonitrile in 0.1% formic acid. The MS was operated in information-dependent acquisition mode, scanning full spectra (400–1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100–1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and +5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. Rolling collision energy (CE) was used with a CE spread of 15. The MS was operated by Analyst TF 1.7.1 software (AB Sciex). For data-independent acquisition (SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at a 50-ms accumulation time for m/z 400–1250. MS/MS SWATH scans were set at 5-Da windows that overlapped by 1 Da for m/z 400–1250 and varied on each side of the mass range. The total cycle time was 9.6 s. Rolling CE parameter script was used for automatically controlling the CE.
Data Analysis—Acquired spectra were searched against the UniProt reviewed database using the Paragon algorithm embedded in ProteinPilot 5.0.1 software (AB Sciex), with the following search parameters: (i) sample type: identification, (ii) Cys alkylation: iodoacetamide, (iii) digestion: trypsin, (iv) instrument: TripleTOF 6600, (v) species: Mus musculus, (vi) ID focus: biological modifications, (vii) detected protein threshold: >0.05 (10% confidence). The detected protein threshold was set to the minimum level to enhance the number of wrong answers to enable the curve fitting by an independent false discovery rate (FDR) analysis45. This was carried out by the target-decoy approach provided with ProteinPilot software, which was used to assess the quality of the identifications. Identifications were considered positive when identified proteins and peptides reached a 1% local FDR46. The resulting .group file was loaded into Peakview (v2.2.0, AB Sciex), and peaks from SWATH runs were extracted with a peptide confidence threshold of 99% and a FDR <1%. The SWATH files were then exported to MarkerView software (version 1.3.0.1; AB Sciex), and peak areas of individual peptides were normalized to the sum of peak areas of all detected peptides. Statistics of PCA and OPLS-DA were performed using Simca software (Infocom Corp., Tokyo, Japan) for multivariate statistical analysis. Pareto scaling was applied to the peak area values acquired by SWATH prior to the analyses, which represents a compromise between the extremes of no scaling and unit variance scaling and involves dividing each spectral variable by the square root of its standard deviation after first centering.
2022-05-12 | PXD025953 | JPOST Repository
Project description:Concentration of extracted proteins were determined by BCA method using albumin as a standard. Sample volume was adjusted so that the each sample contain 20 μg protein, and proteins were precipitated with chilled acetone. The pellet was resuspended with 40 μl of 50 mM ammonium bicarbonate containing 50% trifluoroethanol and reduced with 1 μl of 200 mM dithiothreitol (DTT). The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 4 μl of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 1 μl of 200 mM DTT. The samples were then diluted with 300 μl of 50 mM ammonium bicarbonate and incubated with 1 μg trypsin (TPCK treated, AB Sciex, Framingham, MA, USA) at 37 °C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid (FA) and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to an TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography with a trap and elution configuration using a nano trap column (350 μm × 0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse phase column (75 μm × 15 cm, 3 μm, 120 Å, AB Sciex) at 300 nl/min with a 90 min linear gradient of 8-30% acetonitrile in 0.1% FA, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% FA. The mass spectrometer was operated in information-dependent acquisition (IDA) mode, scanning full spectra (400–1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100–1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. Rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated using the Analyst TF 1.7.1 software program (AB Sciex). For data dependent acquisition (DDA, SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at 50 ms accumulation time for m/z 400–1250. MS/MS SWATH scans were set at 5 Da window overlapping by 1 Da for m/z 400–1250 and varied on each side of the mass range. The total cycle time was 9.6 s. A rolling collision energy (CE) parameters script was used to automatically control the CE.
Acquired spectra were searched against the UniProt reviewed database using the Paragon algorithm embedded in the ProteinPilot 5.0.1 software program (AB Sciex), with the following search parameters: (i) sample type: identification, (ii) Cys alkylation: iodoacetamide, (iii) digestion: trypsin, (iv) instrument: TripleTOF 6600, (v) species: Homo sapiens, (vi) ID focus: biological modifications, (vii) detected protein threshold: > 0.05 (10% confidence). The detected protein threshold was set to the minimum level to enhance the number of wrong answers to enable the curve fitting by an independent FDR analysis(1). This was carried out by the target-decoy approach provided with the ProteinPilot software program, which was used to assess the quality of the identifications. Positive identifications were considered when identified proteins and peptides reached a 1% local FDR(2). The resulting group file was loaded into Peakview (v2.2.0, AB Sciex) and peaks from SWATH runs were extracted with a peptide confidence threshold of 99% and a false discovery rate <1%. The SWATH files were then exported to the MarkerView software program (version 1.3.0.1; AB Sciex) and the peak areas of individual peptides were normalized to the sum of the peak areas of all detected peptides.
2022-05-20 | PXD026109 | JPOST Repository
Project description:Mitochondrial fraction was obtained using the mitochondrial isolation kit (KC010100, BioChain Institute). Each tissue was finely chopped and homogenized 40 strokes in two volumes of mitochondrial isolation buffer, and then centrifuged at 600×g for 10 min. The supernatant was collected and centrifuged at 12,000×g for 15 min. The supernatant was used as cytosolic fraction containing lysosomes and microsomes. The mitochondrial fraction was obtained from the pellet and resuspended in mitochondrial isolation buffer. The suspended mitochondria were sonicated (TOMY, Ultrasonic disruptor UD-100, output level 30, 30 sec×2) and centrifuged at 105,000×g for 30 min. The supernatant was used as the mitochondrial soluble fractions, containing mitochondrial intermembrane space (IMS) and matrix (MAT). The pellet was resuspended in RIPA buffer and centrifuged at 20,000×g for 30 min. The supernatant was used as the mitochondrial membrane fractions, containing mitochondrial outer membrane (OM) and inner membrane (IM). All the procedures were performed at 4°C.
Mitochondrial and cytosolic fractions of WT and ES1-KO mouse brain were isolated as described 2.1 in 1% triton x-100 in 20 mM Tris-HCl. These samples were concentrated by SDS-PAGE and cut out from gels. The sectioned gels were finely chopped and washed with water. Then, the gel pieces were destained 50% methanol and vortexed in 25 mM ammonium bicarbonate containing 50% acetonitrile for 5 min. The supernatant was removed and the gel pieces were soaked 100% acetonitrile for 1 min. After removing the solution, the gel pieces were dried in vacuo, and rehydrated with a reducing solution (50 mM ammonium bicarbonate and 25 mM dithiothreitol), and incubated for 40 min at 56°C. The reducing buffer was removed and gel pieces were soaked in an alkylating solution (50 mM ammonium bicarbonate containing 55 mM iodoacetamide) for 30 min at room temperature in the dark. After removing the alkylation solution, the gel pieces were washed twice with water and vortexed in 25 mM ammonium bicarbonate containing 50% acetonitrile for 5 min, and then soaked 100% acetonitrile for 1 min. After removing the solution, the gel pieces were dried in vacuo and rehydrated with 50 mM ammonium bicarbonate containing 4 ng/μL sequencing grade trypsin and 0.01% Protease Max Surfactant. After incubating 10 min on ice, an equivalent volume of 50 mM ammonium bicarbonate containing 0.01% Protease Max Surfactant was added and incubated for 3 h at 37°C to digest the proteins in the gels with a protease. The equivalent volume of 1% trifluoroacetic acid was added and vortexed for 10 min for extraction of the tryptic fragments. After centrifuged at 12,000×g for 15 min, the peptide solutions were obtained from the supernatant.
Ten microliters of each peptide solution were diluted with 190 μL of 100 mM ammonium bicarbonate and filtered on with a 0.22 μm using the amicon ultrafiltration unit (Amicon Ultra, 3 kDa, Millipore, MA, USA). Concentrated samples were denatured with an equivalent volume of trifluoroethanol (25 μL) and reduced with 1 μL of 200 mM dithiothreitol (DTT). The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 4 μL of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 1 μL of 200 mM DTT. The samples were then mixed with 300 μL of 100 mM ammonium bicarbonate. Fifteen microliters of the sample were diluted with 85 μL of 100 mM ammonium bicarbonate and incubated with 1 μg trypsin (TPCK treated, AB Sciex, Framingham, MA, USA) at 37 °C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid (FA) and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography with a trap and elution configuration using a nano trap column (350 μm×0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm×15 cm, 3 μm, 120 Å, AB Sciex) at 300 nL/min with a 90 min linear gradient of 8-30% acetonitrile in 0.1% FA, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% FA. The mass spectrometer was operated in information-dependent acquisition (IDA) mode, scanning full spectra (400–1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100–1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. The rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated using the Analyst TF 1.7.1 software program (AB Sciex). For data-dependent acquisition (DDA, SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at 50 ms accumulation time for m/z 400–1250. MS/MS SWATH scans were set at 5 Da window overlapping by 1 Da for m/z 400–1250 and varied on each side of the mass range. The total cycle time was 9.6 s. Rolling collision energy (CE) parameter script was used to automatically control the CE.
Acquired spectra were searched against the UniProt reviewed database using the Paragon algorithm embedded in the ProteinPilot 5.0.1 software program (AB Sciex), with the following search parameters: (i) sample type: identification, (ii) Cys alkylation: iodoacetamide, (iii) digestion: trypsin, (iv) instrument: TripleTOF 6600, (v) species: Mus musculus, (vi) ID focus: biological modifications, (vii) detected protein threshold: > 0.05 (10% confidence). The detected protein threshold was set to the minimum level to enhance the number of wrong answers to enable the curve fitting by an independent FDR analysis. This was carried out by the target-decoy approach provided with the ProteinPilot software program, which was used to assess the quality of the identifications. Positive identifications were considered when identified proteins and peptides reached a 1% local FDR. The resulting group file was loaded into Peakview (v2.2.0, AB Sciex) and peaks from SWATH runs were extracted with a peptide confidence threshold of 99% and a false discovery rate <1%. The SWATH files were then exported to the MarkerView software program (version 1.3.0.1; AB Sciex) and the peak areas of individual peptides were normalized to the sum of the peak areas of all detected peptides.
2022-05-12 | PXD025954 | JPOST Repository
Project description:Mitochondrial fraction was obtained using the mitochondrial isolation kit (KC010100, BioChain Institute). Each tissue was finely chopped and homogenized 40 strokes in two volumes of mitochondrial isolation buffer, and then centrifuged at 600×g for 10 min. The supernatant was collected and centrifuged at 12,000×g for 15 min. The supernatant was used as cytosolic fraction containing lysosomes and microsomes. The mitochondrial fraction was obtained from the pellet and resuspended in mitochondrial isolation buffer. The suspended mitochondria were sonicated (TOMY, Ultrasonic disruptor UD-100, output level 30, 30 sec×2) and centrifuged at 105,000×g for 30 min. The supernatant was used as the mitochondrial soluble fractions, containing mitochondrial intermembrane space (IMS) and matrix (MAT). The pellet was resuspended in RIPA buffer and centrifuged at 20,000×g for 30 min. The supernatant was used as the mitochondrial membrane fractions, containing mitochondrial outer membrane (OM) and inner membrane (IM). All the procedures were performed at 4°C.
Mitochondrial and cytosolic fractions of WT and ES1-KO mouse brain were isolated as described 2.1 in 1% triton x-100 in 20 mM Tris-HCl. These samples were concentrated by SDS-PAGE and cut out from gels. The sectioned gels were finely chopped and washed with water. Then, the gel pieces were destained 50% methanol and vortexed in 25 mM ammonium bicarbonate containing 50% acetonitrile for 5 min. The supernatant was removed and the gel pieces were soaked 100% acetonitrile for 1 min. After removing the solution, the gel pieces were dried in vacuo, and rehydrated with a reducing solution (50 mM ammonium bicarbonate and 25 mM dithiothreitol), and incubated for 40 min at 56°C. The reducing buffer was removed and gel pieces were soaked in an alkylating solution (50 mM ammonium bicarbonate containing 55 mM iodoacetamide) for 30 min at room temperature in the dark. After removing the alkylation solution, the gel pieces were washed twice with water and vortexed in 25 mM ammonium bicarbonate containing 50% acetonitrile for 5 min, and then soaked 100% acetonitrile for 1 min. After removing the solution, the gel pieces were dried in vacuo and rehydrated with 50 mM ammonium bicarbonate containing 4 ng/μL sequencing grade trypsin and 0.01% Protease Max Surfactant. After incubating 10 min on ice, an equivalent volume of 50 mM ammonium bicarbonate containing 0.01% Protease Max Surfactant was added and incubated for 3 h at 37°C to digest the proteins in the gels with a protease. The equivalent volume of 1% trifluoroacetic acid was added and vortexed for 10 min for extraction of the tryptic fragments. After centrifuged at 12,000×g for 15 min, the peptide solutions were obtained from the supernatant.
Ten microliters of each peptide solution were diluted with 190 μL of 100 mM ammonium bicarbonate and filtered on with a 0.22 μm using the amicon ultrafiltration unit (Amicon Ultra, 3 kDa, Millipore, MA, USA). Concentrated samples were denatured with an equivalent volume of trifluoroethanol (25 μL) and reduced with 1 μL of 200 mM dithiothreitol (DTT). The samples were incubated at 90°C for 30 min and cooled to room temperature. Free cysteine residues were alkylated with 4 μL of 200 mM iodoacetamide for 60 min at room temperature in the dark and the remaining iodoacetamide was quenched by adding 1 μL of 200 mM DTT. The samples were then mixed with 300 μL of 100 mM ammonium bicarbonate. Fifteen microliters of the sample were diluted with 85 μL of 100 mM ammonium bicarbonate and incubated with 1 μg trypsin (TPCK treated, AB Sciex, Framingham, MA, USA) at 37 °C for 18 h. The samples were desalted with C18 ZipTip (Millipore, Bedford, MA, USA) and eluted with H2O/acetonitrile (5/5; v/v). The ZipTip eluates were dried in a vacuum centrifuge. Desalted samples were rehydrated in 0.1% formic acid (FA) and were analyzed by LC-MS using a nanoLC Eksigent 400 system (Eksigent, AB Sciex), coupled online to a TripleTOF6600 mass spectrometer (AB Sciex). Peptide separation was performed using liquid chromatography with a trap and elution configuration using a nano trap column (350 μm×0.5 mm, 3 μm, 120 Å, AB Sciex) and a nano ChromXP C18 reverse-phase column (75 μm×15 cm, 3 μm, 120 Å, AB Sciex) at 300 nL/min with a 90 min linear gradient of 8-30% acetonitrile in 0.1% FA, and then, with a 10 min linear gradient of 30% to 40% acetonitrile in 0.1% FA. The mass spectrometer was operated in information-dependent acquisition (IDA) mode, scanning full spectra (400–1500 m/z) for 250 ms, followed by up to 30 MS/MS scans (100–1800 m/z for 50 ms each), for a cycle time of 1.8 s. Candidate ions with a charge state between +2 and + 5 and counts above a minimum threshold of 125 counts per second were isolated for fragmentation, and one MS/MS spectrum was collected before adding those ions to the exclusion list for 12 s. The rolling collision energy was used with a collision energy spread of 15. The mass spectrometer was operated using the Analyst TF 1.7.1 software program (AB Sciex). For data-dependent acquisition (DDA, SWATH acquisition), the parameters were set as follows: 100 ms TOF MS scan, followed by 200 variable SWATH windows each at 50 ms accumulation time for m/z 400–1250. MS/MS SWATH scans were set at 5 Da window overlapping by 1 Da for m/z 400–1250 and varied on each side of the mass range. The total cycle time was 9.6 s. Rolling collision energy (CE) parameter script was used to automatically control the CE.
Acquired spectra were searched against the UniProt reviewed database using the Paragon algorithm embedded in the ProteinPilot 5.0.1 software program (AB Sciex), with the following search parameters: (i) sample type: identification, (ii) Cys alkylation: iodoacetamide, (iii) digestion: trypsin, (iv) instrument: TripleTOF 6600, (v) species: Mus musculus, (vi) ID focus: biological modifications, (vii) detected protein threshold: > 0.05 (10% confidence). The detected protein threshold was set to the minimum level to enhance the number of wrong answers to enable the curve fitting by an independent FDR analysis. This was carried out by the target-decoy approach provided with the ProteinPilot software program, which was used to assess the quality of the identifications. Positive identifications were considered when identified proteins and peptides reached a 1% local FDR. The resulting group file was loaded into Peakview (v2.2.0, AB Sciex) and peaks from SWATH runs were extracted with a peptide confidence threshold of 99% and a false discovery rate <1%. The SWATH files were then exported to the MarkerView software program (version 1.3.0.1; AB Sciex) and the peak areas of individual peptides were normalized to the sum of the peak areas of all detected peptides.
2022-05-12 | PXD025963 | JPOST Repository
Project description:Twenty million LbetaT2 cells were transfected with either control or Galphas siRNA, then were seeded in 100-mm cell culture plates in DMEM + 10% FBS. Two days later, cells were washed twice with pre-warmed PBS. Conditioned media was harvested another 24 h later, and centrifuged at 20,000 g for 10 min at 4°C to remove cell debris. To enrich secreted proteins in the conditioned media, conditioned media samples were centrifuged using Amicon centrifugal filters with a 3kDa cutoff (Millipore, Billerica, MA). A total of 8 concentrated conditioned media samples were independently prepared: 4 samples from control siRNA-treated cells, and 4 samples from Galphas siRNA-treated cells. Samples were stored at –70°C until they were sent to the Mount Sinai Proteomics Core Facility.HPLC-isobaric tags for relative and absolute quantitation mass-spectrometry (iTRAQ MS) - Data analysis ProteinPilot 3.0 (AB Sciex) was used to search the MS/MS spectra for protein identification and quantitation with its searching algorithm Paragon 3.0.0.0 (*Reference). The protein database used for searching was Uniprot mouse fasta file (release-2010_11). The search parameters include quantitation for iTRAQ 8-plex (peptide-labeled), MMTS for cysteine alkylation, trypsin for enzyme digestion, biological modifications for ID focus, and taxonomy set for Mus musculus. The detected protein threshold was set to 1.3 (95% confidence). Additionally, we converted our AB Sciex mass spectral data (TOF/TOF data) into an mzML format, using the AB Sciex MS Data Converter (beta version 1.3) tool. Finally, we used the command line tool group2xml, which is included with ProteinPilot Software, to convert the .group search engine result file to an XML file.
2016-09-27 | PXD000063 | Pride