G***G 发帖数: 16778 | 1 thanks. I used OMSSA before. did you use it?
do you know how to get peptide quantition from OMSSA?
is it easy to get peptide/protein quantition from x!tandem? |
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G***G 发帖数: 16778 | 3 I am using OMSSA now.
which output parameter is the peptide intensity or protein intensity? |
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s****a 发帖数: 1039 | 4 do u want to do peptide quantitation?
use X!Tandem or OMSSA first and use the quantitation function of TPP. You
shall get the intensity information. |
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k****o 发帖数: 728 | 5 如果你的peptide比较长,以至于产生很多+3--+5甚至更高的fragment ions,那么无论
对于ETD还是CID,在OT里做high resolution的MS2都更有利。而ETD是有利于high
charge state,long peptide的fragmentation。所以,如果你的样品确实有很多long
peptide的话(你去raw data file,average一段MS1的data就有底了),用OT scan
MS2会让搜索效果更好。你搜索时记得把fragment ions的error window舍得很窄,这样
才起到high resolution的效果。比如10 or 20ppm,或者0.01 m/z,取决于你具体的
accuracy。你可以试试MS2用15000 resolution with 20 ppm error window。
关于省时间的问题。诚然IT确实比OT省时间,如果你用老一代的LTQ Orbitrap,这个确
实是个大concern。但技术在进步,Orbitrap Fusion已经在设计上提供了比过去快得多
的ion transmi... 阅读全帖 |
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