STEM
What is STEM?
STEM is the software that efficiently processes large-scale mass spectrometry-based proteomics data. V-mode evaluates the Mascot peptide identification dataset, removes unreliable candidates and redundant assignments, and integrates the results of experiments. C-mode compares peptide coverage among multiple datasets and displays proteins commonly/specifically found therein, and processes data for quantitative studies that utilize conventional isotope tags or tags having a smaller mass difference. STEM significantly improves proteomic throughput.
Version History
- Ver2.1.1 / 060202/ This version of STEM can process the data from Mascot 2.1.3.
- Ver2.1 / 060202/ This version of STEM can process the data from Mascot 2.1. The STEM manual (ver 2.1) was also released.
- Ver2.0.3 / 060127 / This version of STEM can process the data when arrangement of files in the Mascot server is not default. The STEM manual (ver 2.0.3) was also released.
- Ver2.0.2 / 060125 / We fixed the bug caused by latest update of STEM.
- Ver2.0.1 / 060123 / This version of STEM can process the data generated by the UNIX Mascot.
- Ver2.0 / 051226 / STEM was relesed with English manual. The GUI of STEM was renewed.
- Ver1.0.1 / 051018 / STEM was uploaded with Japanese manual.
References
Original article
- Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T.
STEM: A Software Tool for Large-Scale Proteomic Data Analyses.
J Proteome Res. 2005 Oct 10;4(5):1826-1831.
Other articles (MS data processed by STEM)
- Nunomura K, Nagano K, Itagaki C, Taoka M, Okamura N, Yamauchi Y, Sugano S, Takahashi N, Izumi T, Isobe T.
Cell surface labeling and mass spectrometry reveal diversity of cell-surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells.
Mol Cell Proteomics. 2005 Dec;4(12):1968-1976.
- Nagano K, Taoka M, Yamauchi Y, Itagaki C, Shinkawa T, Nunomura K, Okamura N, Takahashi N, Izumi T, Isobe T.
Large-scale identification of proteins expressed in mouse embryonic stem cells.
Proteomics. 2005 Apr;5(5):1346-61.
- Ichimura T, Yamamura H, Sasamoto K, Tominaga Y, Taoka M, Kakiuchi K, Shinkawa T, Takahashi N, Shimada S, Isobe T.
14-3-3 proteins modulate the expression of epithelial Na+ channels by phosphorylation-dependent interaction with Nedd4-2 ubiquitin ligase.
J Biol Chem. 2005 Apr 1;280(13):13187-94. - Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, Nakayama H, Takahashi N, Isobe T.
Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins.
Mol Cell Proteomics. 2004 Aug;3(8):780-7. - Yanagida M, Hayano T, Yamauchi Y, Shinkawa T, Natsume T, Isobe T, Takahashi N.
Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes.
J Biol Chem. 2004 Jan 16;279(3):1607-14. - Yoshimura Y, Yamauchi Y, Shinkawa T, Taoka M, Donai H, Takahashi N, Isobe T, Yamauchi T.
Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry.
J Neurochem. 2004 Feb;88(3):759-68. - Hayano T, Yanagida M, Yamauchi Y, Shinkawa T, Isobe T, Takahashi N.
Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome.
J Biol Chem. 2003 Sep 5;278(36):34309-19. - Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T.
Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins.
Nat Biotechnol. 2003 Jun;21(6):667-72. - Mawuenyega KG, Kaji H, Yamuchi Y, Shinkawa T, Saito H, Taoka M, Takahashi N, Isobe T.
Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry.
J Proteome Res. 2003 Jan-Feb;2(1):23-35.
