Fourier Transform Infrared (FTIR) and X-ray Fluorescence (XRF) were used to measure organic functional groups and elements of submicron particles collected during MILAGRO in March 2006 on three platforms: the Mexico City urban area (SIMAT), the high altitude site at 4010 m (Altzomoni), and the NCAR C130 aircraft. Scanning transmission X-ray Microscopy (STXM) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) were applied to single particle organic functional group abundance analysis of particles simultaneously collected at SIMAT and C130. Correlations of elemental concentrations showed different groups of source related elements at SIMAT, Altzomoni, and C130, suggesting different processes affecting the air masses sampled at the three platforms. Cluster analysis resulted in seven distinct Clusters of FTIR spectra, with the last three clusters consisting of spectra collected almost exclusively on the C130 platform, reflecting the variety of sources contributing to C130 samples. Positive Matrix Factorization (PMF) of NEXAFS-STXM spectra identified three main factors representing soot, secondary, and biomass burning type spectra. PMF of FTIR spectra resulted in three fossil fuel combustion type factors, one biomass burning factor, and one mixed or processed factor. The fossil fuel combustion type factors were found to have the largest contributions to OM, while the processed factor has the largest O/C among all factors. Alkane, carboxylic acid, and amine functional groups were mainly associated with combustion related sources, while alcohol groups were likely from atmospheric processing of mixed sources. While the processed factor has the highest O/C, half of the OM and O/C measured could be attributed directly to fossil fuel combustion sources. Both PMF of NEXAFS-STXM spectra and PMF of FTIR spectra indicate that the combustion type factors are more affected by fluctuations in local sources, while the processed factors are more consistent during the sampling period.