Hello there,
I know that shotgun proteomics relies on high-resolution instruments (i.e. Orbitrap and New QTof systems) with nano-LC flow and nano-ESI mostly, however I only have a reach to a Microflow LC with an older QTof (Waters Micromass Micro). These instruments work fine, however I recently discovered that the resolution of the QTof is slightly higher than 5000 FWHM, which is much lower than today's QTof instruments.
I'm planning on using the SILAC (where isotopic amino acids are used) technique to determine the regulated proteins in my human cell samples. I'm not going to discover a protein which was not discovered before or anything.
How reliable using this LC-QTof system will be in my studies? Will software such as MaxQuant be able to determine the proteins which are regulated in my protein samples, or will the low resolution and high LC flow rate be a problem?