Abstract:
:LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw data processing, which utilizes precursor-level high mass accuracy data for peak processing and MGF creation. In particular, ProteinPilot results from MaxQuant-processed peaklists for Orbitrap data sets resulted in improved spectral utilization due to an improved peaklist quality with higher precision and high precursor mass accuracy (HPMA). The output and postsearch analysis tools of both workflows were utilized for previously unexplored features of a three-dimensional fractionated and hexapeptide library (ProteoMiner) treated whole saliva data set comprising 200 fractions. ProteinPilot's ability to simultaneously predict multiple modifications showed an advantage from ProteoMiner treatment for modified peptide identification. We demonstrate that complementary approaches in the analysis pipeline provide comprehensive results for the whole saliva data set acquired on an LTQ Orbitrap. Overall our results establish a workflow for improved protein identification from high mass accuracy data.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Jagtap P,Bandhakavi S,Higgins L,McGowan T,Sa R,Stone MD,Chilton J,Arriaga EA,Seymour SL,Griffin TJdoi
10.1002/pmic.201100097subject
Has Abstractpub_date
2012-06-01 00:00:00pages
1726-30issue
11eissn
1615-9853issn
1615-9861journal_volume
12pub_type
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