@article {Meyer141382, author = {Jesse G. Meyer and Sushanth Mukkamalla and Hanno Steen and Alexey I. Nesvizhskii and Bradford W. Gibson and Birgit Schilling}, title = {PIQED: Automated Identification and Quantification of Protein Modifications from DIA-MS Data}, elocation-id = {141382}, year = {2017}, doi = {10.1101/141382}, publisher = {Cold Spring Harbor Laboratory}, abstract = {To the editor: Label-free quantification using mass spectrometric data-independent acquisition (DIA) is a robust method for deep and accurate proteome quantification1. Here we report a workflow and open-source software tool with a graphical user interface (GUI), PIQED, to enable completely automated Post-translational modification (PTM) Identification and Quantification Exclusively from DIA (figure 1a; https://github.com/igmeverucsd/PIQEDia/releases/tag/v0.1.2).}, URL = {https://www.biorxiv.org/content/early/2017/05/24/141382}, eprint = {https://www.biorxiv.org/content/early/2017/05/24/141382.full.pdf}, journal = {bioRxiv} }