Supplemental Material 1


Formatting details of the sample flat-file

Here are two entries in the sample flat-file located on the data acquisition component shown as an example:


D:\XCalibur\Data\PVJurkatbeadtest _newbeads_030309_030606+FT+human_FT_phos_alkyl.params+username+dd_top5_cc_92acq_FTMSLTMSMScss.meth+SQ:1002


#: a preceding mark that turns on/off an entry in the queue. The entry with # means it has already been processed.

D:\XCalibur\Data\JurkatPV_beadtest_030809_211726: path and file name (without extension) for the acquired raw file

FT: a parameter to represent the instrument type. FT: high mass accuracy mass spec; LT: low mass accuracy mass spec

human_FT_phos_alkyl.params: designated SEQUEST database search parameter file

username: a username for the sample owner

dd_top5_cc_92acq_FTMSLTMSMScss.meth: mass spec method used to acquire this raw file

SQ:1002: id number of this sample in the Filemaker sample queue database

In the second queue file located downstream of the database search component on the data loader, each entry contains filename only.

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