PXD025950

PXD025950 is an original dataset announced via ProteomeXchange.

Title	SWATH-MS analysis of x-ray radiated mouse serum
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.
HostingRepository	jPOST
AnnounceDate	2022-05-12
AnnouncementXML	Submission_2023-03-14_16:40:35.413.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yota Tatara
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxamidomethyl-L-cysteine; N6-acetyl-L-lysine; alpha-amino acetylated residue; 2-pyrrolidone-5-carboxylic acid (Gln); 2-pyrrolidone-5-carboxylic acid (Glu); L-methionine sulfoxide; phosphorylated L-histidine; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-11 21:00:45	ID requested
1	2022-05-11 08:00:24	announced
2	2022-09-18 02:52:59	announced	2022-09-18: Updated FTP location.
⏵ 3	2023-03-14 16:40:36	announced	2023-03-15: Updated PubMed.

Yamaguchi M, Tatara Y, Nugraha ED, Sato Y, Miura T, Hosoda M, Syaifudin M, Tokonami S, Kashiwakura I, Serum Proteomic and Oxidative Modification Profiling in Mice Exposed to Total Body X-Irradiation. Antioxidants (Basel), 11(9):(2022) [pubmed]

submitter keyword: mouse, serum, SWATH, radiation

Ikuo Kashiwakura
lab head
Yota Tatara
contact affiliation	Hirosaki University
dataset submitter

jPOST dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST001168/