In:
PROTEOMICS, Wiley, Vol. 14, No. 2-3 ( 2014-02), p. 169-180
Abstract:
The MS E (where MS E is low energy ( MS ) and elevated energy ( E ) mode of acquisition) acquisition method commercialized by Waters on its Q ‐ TOF instruments is regarded as a unique data‐independent fragmentation approach that improves the accuracy and dynamic range of label‐free proteomic quantitation. Due to its special format, MS E acquisition files cannot be independently analyzed with most widely used open‐source proteomic software specialized for processing data‐dependent acquisition files. In this study, we established a workflow integrating S kyline, a popular and versatile peptide‐centric quantitation program, and a statistical tool DiffProt to fulfill MS E ‐based proteomic quantitation. Comparison with the vendor software package for analyzing targeted phosphopeptides and global proteomic datasets reveals distinct advantages of Skyline in MS E data mining, including sensitive peak detection, flexible peptide filtering, and transparent step‐by‐step workflow. Moreover, we developed a new procedure such that S kyline MS 1 filtering was extended to small molecule quantitation for the first time. This new utility of Skyline was examined in a protein–ligand interaction experiment to identify multiple chemical compounds specifically bound to NDM ‐1 (where NDM is N ew D elhi metallo‐β‐lactamase 1), an antibiotics‐resistance target. Further improvement of the current weaknesses in S kyline MS 1 filtering is expected to enhance the reliability of this powerful program in full scan‐based quantitation of both peptides and small molecules.
Type of Medium:
Online Resource
ISSN:
1615-9853
,
1615-9861
DOI:
10.1002/pmic.v14.2-3
DOI:
10.1002/pmic.201300352
Language:
English
Publisher:
Wiley
Publication Date:
2014
detail.hit.zdb_id:
2037674-1
SSG:
12
