One of the small hidden details in publications, even in those with a higher impact, is the use of "in-house programs". What is an "in-house" program or tool: Normally is a piece of software that researchers use to analyze process or visualize the experimental data, but most important the software it-self is not published.
The term by itself is inoffensive, but the concept could be extremely dangerous. We can cite hundreds of manuscripts that included in the data analysis "in-house" tools, but never the terms "in-house instruments". The authors always needs to cite the manufacturer, the reagents, even the year and the company. I know, we have a section to describe data processing but mostly we cite some parameters, and the well known software like search engines (Mascot, X!Tandem, Sequest, etc). But at some point of this section several times you can find the term "in-house" tool. It could be a reference to an excel formula or to a complete and complex java program with many tasks like parsing a search engine output, computing the FDR, removing false-positive identifications, computing peptide-spectrum-match redundancy, etc. The are not a real/objective measure to distinguish between a little-simple tool and a complex tool one.