PT  - JOURNAL ARTICLE
AU  - Jesse G. Meyer
AU  - Sushanth Mukkamalla
AU  - Alexandria K. D’Souza
AU  - Alexey I. Nesvizhskii
AU  - Bradford W. Gibson
AU  - Birgit Schilling
TI  - DIA-Pipe: Identification and Quantification of Post-Translational Modifications using exclusively Data-Independent Acquisition
AID  - 10.1101/141382
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 141382
4099  - http://biorxiv.org/content/early/2017/05/25/141382.short
4100  - http://biorxiv.org/content/early/2017/05/25/141382.full
AB  - Label-free quantification using data-independent acquisition (DIA) is a robust method for deep and accurate proteome quantification1,2. However, when lacking a pre-existing spectral library, as is often the case with studies of novel post-translational modifications (PTMs), samples are typically analyzed several times: one or more data dependent acquisitions (DDA) are used to generate a spectral library followed by DIA for quantification. This type of multi-injection analysis results in significant cost with regard to sample consumption and instrument time for each new PTM study, and may not be possible when sample amount is limiting and/or studies require a large number of biological replicates. Recently developed software (e.g. DIA-Umpire) has enabled combined peptide identification and quantification from a data-independent acquisition without any pre-existing spectral library3,4. Still, these tools are designed for protein level quantification. Here we demonstrate a software tool and workflow that extends DIA-Umpire to allow automated identification and quantification of PTM peptides from DIA. We accomplish this using a custom, open-source graphical user interface DIA-Pipe (https://github.com/jgmeyerucsd/PIQEDia/releases/tag/v0.1.2) (figure 1a).