{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX2_01_20110928_F007446.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX5_01_GPM00300017787.2011_09_28_16_51_27.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX7_01_20110928_F007467.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX1_01_20110928_F007453.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX5_01_20110928_F007457.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT2_01_20130305_F017043.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX3_01_20110928_F007463.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX8_01_20110928_F007460.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX3_01_GPM00300017801.2011_09_28_16_59_37.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX2_02_20111003_F007475.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX6_02_20111003_F007479.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX5_02_GPM00300017811.2011_10_03_10_10_13.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX2_01_GPM00300017800.2011_09_28_16_58_58.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT6_01_20130306_F017047.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX4_02_GPM00300017810.2011_10_03_10_09_50.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX6_02_GPM00300017812.2011_10_03_10_10_28.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX6_01_20110928_F007450.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX8_01_GPM00300017798.2011_09_28_16_56_42.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX7_01_GPM00300017789.2011_09_28_16_51_58.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX4_01_20110928_F007464.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX1_01_GPM00300017791.2011_09_28_16_53_56.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX5_01_GPM00300017795.2011_09_28_16_56_03.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX4_01_20110928_F007456.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX2_02_GPM00300017808.2011_10_03_10_08_41.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT3_01_20130305_F017044.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX7_01_GPM00300017797.2011_09_28_16_56_32.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX2_01_GPM00300017784.2011_09_28_16_49_57.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX7_02_20111003_F007480.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX5_02_20111003_F007478.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX1_01_GPM00300017799.2011_09_28_16_58_13.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT1_02_GPM00300001066.2013_03_06_17_28_16.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT7_01_20130306_F017048.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX8_01_20110928_F007468.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX3_01_20110928_F007447.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT6_01_GPM00300001071.2013_03_06_18_06_34.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX7_01_20110928_F007451.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX3_01_GPM00300017785.2011_09_28_16_50_40.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX5_01_20110928_F007465.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT4_01_GPM00300001069.2013_03_06_17_52_38.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX4_01_GPM00300017786.2011_09_28_16_51_09.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT2_01_GPM00300001067.2013_03_06_17_34_50.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX1_02_20111003_F007474.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX3_01_20110928_F007455.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX1_01_20110928_F007461.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX8_01_GPM00300017790.2011_09_28_16_52_12.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX8_01_GPM00300017806.2011_09_28_17_01_04.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX8_02_GPM00300017814.2011_10_03_10_10_53.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT4_01_20130305_F017045.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX8_02_20111003_F007481.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX7_01_20110928_F007459.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT7_01_GPM00300001072.2013_03_06_18_15_43.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX4_02_20111003_F007477.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX6_01_GPM00300017796.2011_09_28_16_56_17.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT8_01_20130306_F017049.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX2_01_GPM00300017792.2011_09_28_16_54_38.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX3_01_GPM00300017793.2011_09_28_16_55_17.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX4_01_20110928_F007448.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX8_01_20110928_F007452.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX5_01_20110928_F007449.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX1_01_20110928_F007445.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT8_01_GPM00300001073.2013_03_06_18_25_06.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX6_01_20110928_F007466.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX4_01_GPM00300017794.2011_09_28_16_55_44.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT3_01_GPM00300001068.2013_03_06_17_43_30.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX4_01_GPM00300017802.2011_09_28_17_00_04.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX7_02_GPM00300017813.2011_10_03_10_10_41.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX2_01_20110928_F007454.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX6_01_20110928_F007458.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT5_01_GPM00300001070.2013_03_06_17_59_07.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX2_01_20110928_F007462.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX5_01_GPM00300017803.2011_09_28_17_00_23.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX3_02_GPM00300017809.2011_10_03_10_09_16.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX7_01_GPM00300017805.2011_09_28_17_00_51.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT5_01_20130305_F017046.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX3_02_20111003_F007476.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT1_02_20130305_F017042.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX1_02_GPM00300017807.2011_10_03_10_08_06.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX1_01_GPM00300017783.2011_09_28_16_49_12.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX6_01_GPM00300017788.2011_09_28_16_51_45.t.xt.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX6_01_GPM00300017804.2011_09_28_17_00_39.t.xt.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT2_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT6_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX8_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX4_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX4_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX5_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX5_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX4_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX1_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX4_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX3_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX8_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX8_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT7_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT1_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX7_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT8_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT4_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX6_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX6_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX2_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX6_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX2_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX3_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX2_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX3_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX7_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110929_LA_PoolDSarcoma_SCX6_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX2_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX5_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110926_LA_PoolBSarcoma_SCX7_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110927_LA_PoolCSarcoma_SCX1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT5_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT3_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX3_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX7_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX5_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/110921_LA_PoolASarcoma_SCX8_01.raw"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT6_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT5_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT2_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT7_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT8_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT4_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT3_01.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD000617/130204_Sarcoma_TMT1_02.mgf"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["ana.carneiro@med.lu.se"],"submitter":["Ufuk Kirik"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Tmt human sarcoma"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD000617"],"tissue":["Soft Tissue Sarcoma Cell"],"sample_protocol":["UPS and LMS of the extremities and the trunk wall were selected from the Lund Sarcoma Centre (Lund, Sweden). The Lund University research ethics committee granted ethical permission for the study (LU302-02). Patients with metastases at diagnosis and those who had been treated with neoadjuvant chemo- or radiotherapy were excluded. All tumors were reviewed by two experienced sarcoma pathologists, Dr. Pehr Rissler at Lund University Hospital and Dr. Jonathon Fletcher at Harvard Medical School (Boston, MA), according to the WHO classification (15). Data on histopathologic grade, necrosis, vascular invasion, depth, and size were collected in a standardized manner. LMS diagnosis required the presence of eosinophilic spindle cells with vesicular, blunt-ended, intended, or lobulated nuclei arranged in a fascicular pattern, accounting for 5% to 10% of the surface area examined. Tumors with these characteristics were also required to show unequivocal positivity for smooth-muscle actin (SMA) as well as for desmin and/or h-caldesmon. MFH/UPS were defined as pleomorphic spindle-cell sarcomas without any specific differentiation. These tumors were also negative for melanocytic and hematopoietic markers. Adequate tissue samples and clinical data were available from all cases. Myofibroblastic sarcoma was a pleomorphic spindle-cell sarcoma with either storiform or fascicular growth patterns composed mainly of cells with pale or moderately eosinophilic cytoplasm (without sharply defined cell borders) and pointed, tapering, or somewhat wavy hyperchromatic nuclei. In undoubted cases, there was always widespread positivity for HHF-35 or SMA but not for desmin, and the nuclear features were not convincing for leiomyosarcoma. Tumor blocks were obtained with 1 cm intervals from the entire specimen and all available blocks were analyzed using 4 mm sections. All tumors were stained at the Department of Pathology, Ska ne University Hospital (Lund, Sweden)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":["iodoacetamide derivatized residue","TMT6plex-126 reporter+balance reagent acylated residue"],"data_protocol":["An ESI-LTQ-Orbitrap XL mass spectrometer (Thermo Electron) interfaced with an Eksigent nanoLC plus HPLC system (Eksigent Technologies) was used for all analyses. Peptides were loaded a constant flow rate of 10 mL/minute onto a precolumn (PepMap 100, C18, 5 mm, 5 mm 0.3 mm, LC Packings) and subsequently separated on a 10 mm fused silica emitter, 75 mm 16 cm (PicoTip Emitter, New Objective, Inc.), packed in-house with Reprosil-Pur C18-AQ resin (3 mm Dr. Maisch GmbH). Peptides were eluted with a 150-minute (label-free quantification) or a 90-minute (TMT quantification) linear gradient of 3% to 35% acetonitrile in water, containing 0.1% formic acid, with a flow rate of 300 nL/minute. The Linear Trap Quadrupole (LTQ)-Orbitrap was operated in a data-dependent mode simultaneously acquiringMS spectra in the Orbitrap (from m/z 400 to 2,000) andMS/MS spectra in the LTQ. For the label-free analysis, four MS/MS spectra were acquired using collision-induced dissociation (CID) in the LTQ and each Orbitrap-MS scan was acquired at 60,000FWHMnominal resolution settings using the lock mass option (m/z 445.120025) for internal calibration. For the TMT quantification analysis, the instrument selected three precursor ions for sequential fragmentation by CID and higher-energy collisional dissociation (HCD), for analysis in the LTQ and Orbitrap (recorded at a resolution of 15,000), respectively. The normalized collision energy was set to 35% for CID and 45%HCD. The dynamic exclusion list was restricted to 500 entries using a repeat count of two with a repeat duration of 20 seconds and with a maximum retention period 120 seconds. Precursor ion charge state screening was enabled to select for ions with at least two charges and rejecting ions with undetermined charge state. Raw mass spectrometric data was independently analyzed in Progenesis LC-MS (Nonlinear Dynamics Ltd, version 4.1.4804) and Proteios SE (version 2.19.0; ref. 17) software platforms. In both cases, runs were aligned and peptide identifications were propagated between runs to minimize missing values. MS/MS spectra of ions with charge þ2/þ3/þ4 between 400 and 1,000 m/z and 27 to 62 minutes were filtered and submitted to Mascot for identification using the UniProt database release 2012 filtered for human. Identifications were filtered with anFDRof 0.05 at the peptide and protein levels. Only proteins with at least one unique peptide were kept in the dataset. Qlucore Omics Explorer (Qlucore AB, version 2.3) software was used for statistical analysis of the protein expression profiles. The functional enrichment analysis was carried out with MetaCore (Thomson Reuters, version 6.14) and DAVID (National Institute of Allergy and Infectious Diseases NIH, version 6.7)."],"omics_type":["Proteomics"],"labhead":["Ana Carneiro"],"instrument_platform":["LTQ Orbitrap"],"labhead_affiliation":["Institute of Clinical Sciences, Department of Oncology, Lund University, Sweden"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["ufuk.kirik@immun.lth.se"],"publication":["25069693 Kirik U, Hansson K, Krogh M, Jönsson M, Nilbert M, James P, Carneiro A. Discovery-based protein expression profiling identifies distinct subgroups and pathways in leiomyosarcomas. Mol Cancer Res. 2014 12(12):1729-1739 10.1158/1541-7786.mcr-14-0072"],"curator_keywords":["Biomedical"],"submitter_affiliation":["Department of Immunotechnology"],"pubmed_abstract":["