Mass spectrometry data analysis from PRIDE

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9.5 years ago

paulamic ▴ 20

I am interested in analyzing the data from PRIDE archive (Project PXD000838). This study involves Shotgun Proteomics. My goal is to perform preprocessing of the data and then identify the differentially expressed proteins from it.

I started with the rpx package of R.'pxfiles' usage shows the data has 73 files. Every file (except the readme) is in zipped format. Which of the files should be used for the pre-processing and normalization of the data? What packages should I be using for this purpose? I am very novice in this field. Can anyone please suggest me any way?

Thanks in advance.

PRIDE Spectrometry Mass • 2.0k views

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by paulamic ▴ 20

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Is it SILAC-Mass spec?

ADD REPLY • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by Manvendra Singh ★ 2.2k

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No it is a label free differential proteomics LC-MS based.

ADD REPLY • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by paulamic ▴ 20

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