PXD025975

PXD025975 is an original dataset announced via ProteomeXchange.

Title	Pancreatic cancer proteome from paraffin-embedded tissue
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.
HostingRepository	jPOST
AnnounceDate	2021-10-27
AnnouncementXML	Submission_2022-09-18_03:54:44.875.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yota Tatara
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
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	2021-05-12 03:07:23	ID requested
1	2021-12-19 00:24:53	announced
⏵ 2	2022-09-18 03:54:45	announced	2022-09-18: Updated FTP location.

Wakiya T, Ishido K, Kimura N, Nagase H, Yoshizawa T, Morohashi S, Fujita H, Kanda T, Tatara Y, Saruwatari J, Kijima H, Hakamada K, Eukaryotic initiation factor 2 signaling behind neural invasion linked with lymphatic and vascular invasion in pancreatic cancer. Sci Rep, 11(1):21197(2021) [pubmed]

submitter keyword: human, pancreas, paraffin-embedded

Kenichi Hakamada
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/JPST001172/